https://wiki.cebitec.uni-bielefeld.de/brf-software/index.php?action=history&feed=atom&title=EMMAWiki%2FTermsAndConcepts%2FForUsers%2FDatasetsEMMAWiki/TermsAndConcepts/ForUsers/Datasets - Revision history2026-04-21T15:05:15ZRevision history for this page on the wikiMediaWiki 1.39.7https://wiki.cebitec.uni-bielefeld.de/brf-software/index.php?title=EMMAWiki/TermsAndConcepts/ForUsers/Datasets&diff=1085&oldid=prevAdmin: 10 revisions2011-10-26T06:15:05Z<p>10 revisions</p>
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</td></tr></table>Adminhttps://wiki.cebitec.uni-bielefeld.de/brf-software/index.php?title=EMMAWiki/TermsAndConcepts/ForUsers/Datasets&diff=1084&oldid=previmported>VirginieMittard at 12:09, 25 August 20052005-08-25T12:09:28Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= Terms and Concepts: Dataset =</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= Terms and Concepts: Dataset =</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Well, that is just what it says, a set of data, in the special case of EMMA a matrix of numbers. These data might be the output of an external image analysis software like ImaGene, GenePix or a .cel file from the Affymetrix software. These type of data sets are called ''raw data'', as they normally need further processing to be <del style="font-weight: bold; text-decoration: none;">usefull</del>. In the case of a spotted cDNA microarray these datasets must as a minimum contain the foreground and background intensities for each channel. Location information on the exact spot position is also often required, for instance to draw a false colour image of the microarray with the location of the spots to click on. </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Well, that is just what it says, a set of data, in the special case of EMMA a matrix of numbers. These data might be the output of an external image analysis software like ImaGene, GenePix or a .cel file from the Affymetrix software. These type of data sets are called ''raw data'', as they normally need further processing to be <ins style="font-weight: bold; text-decoration: none;">useful</ins>. In the case of a spotted cDNA microarray these datasets must as a minimum contain the foreground and background intensities for each channel. Location information on the exact spot position is also often required, for instance to draw a false colour image of the microarray with the location of the spots to click on. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>While rows of a raw dataset correspond to individual spots on the array, columns correspond to different types of <del style="font-weight: bold; text-decoration: none;">measurments </del>like foreground background and location values. These are called ''QuantitationTypes''. You think of them as simply being column headers for the matrix.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>While rows of a raw dataset correspond to individual spots on the array, columns correspond to different types of <ins style="font-weight: bold; text-decoration: none;">measurements </ins>like foreground background and location values. These are called ''QuantitationTypes''. You think of them as simply being column headers for the matrix.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Several analysis methods like for instance ''Normalization'' will take raw datasets and produce new datasets by computation. These datasets are called ''Transformed Datasets''. In Transformed Datasets often rows do not correspond to individual spots any more but to genes. Of course different ''QuantitationTypes'' also exist for Derived Datasets. Which QuantitationTypes are actually there depends on the chosen analysis method.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Several analysis methods like for instance ''Normalization'' will take raw datasets and produce new datasets by computation. These datasets are called ''Transformed Datasets''. In Transformed Datasets often rows do not correspond to individual spots any more but to genes. Of course different ''QuantitationTypes'' also exist for Derived Datasets. Which QuantitationTypes are actually there depends on the chosen analysis method.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Each Dataset has to be assigned to at least one Experiment. Raw Datasets can also belong to <del style="font-weight: bold; text-decoration: none;">sevaral </del>experiments. They are automatically added to an Experiment when the corresponding Arrays are assigned.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Each Dataset has to be assigned to at least one Experiment. Raw Datasets can also belong to <ins style="font-weight: bold; text-decoration: none;">several </ins>experiments. They are automatically added to an Experiment when the corresponding Arrays are assigned.</div></td></tr>
</table>imported>VirginieMittardhttps://wiki.cebitec.uni-bielefeld.de/brf-software/index.php?title=EMMAWiki/TermsAndConcepts/ForUsers/Datasets&diff=1083&oldid=previmported>VirginieMittard at 12:05, 25 August 20052005-08-25T12:05:43Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= Terms and Concepts: Dataset =</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= Terms and Concepts: Dataset =</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Well, that is just what it says, a set of data, in the special case of EMMA a matrix of numbers. These data might be the output of an external image analysis software like ImaGene, GenePix or a .cel file from the <del style="font-weight: bold; text-decoration: none;">Affy </del>software. These type of data sets are called ''raw data'', as they normally need further processing to be usefull. In the case of a spotted cDNA microarray these datasets must as a minimum contain the foreground and background intensities for each channel. Location information on the exact spot position is also often required, for instance to draw a false colour image of the microarray with the location of the spots to click on. </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Well, that is just what it says, a set of data, in the special case of EMMA a matrix of numbers. These data might be the output of an external image analysis software like ImaGene, GenePix or a .cel file from the <ins style="font-weight: bold; text-decoration: none;">Affymetrix </ins>software. These type of data sets are called ''raw data'', as they normally need further processing to be usefull. In the case of a spotted cDNA microarray these datasets must as a minimum contain the foreground and background intensities for each channel. Location information on the exact spot position is also often required, for instance to draw a false colour image of the microarray with the location of the spots to click on. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>While rows of a raw dataset correspond to individual spots on the array, columns correspond to different types of measurments like foreground background and location values. These are called ''QuantitationTypes''. You think of them as simply being column headers for the matrix.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>While rows of a raw dataset correspond to individual spots on the array, columns correspond to different types of measurments like foreground background and location values. These are called ''QuantitationTypes''. You think of them as simply being column headers for the matrix.</div></td></tr>
</table>imported>VirginieMittardhttps://wiki.cebitec.uni-bielefeld.de/brf-software/index.php?title=EMMAWiki/TermsAndConcepts/ForUsers/Datasets&diff=1082&oldid=previmported>VirginieMittard at 13:01, 23 August 20052005-08-23T13:01:24Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 15:01, 23 August 2005</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= Terms and Concepts: Dataset =</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= Terms and Concepts: Dataset =</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Well, that is just what it says, a set of data, in the special case of EMMA a matrix of numbers. These data might be the output of an external image analysis software like <del style="font-weight: bold; text-decoration: none;">[[</del>ImaGene<del style="font-weight: bold; text-decoration: none;">]]</del>, <del style="font-weight: bold; text-decoration: none;">[[</del>GenePix<del style="font-weight: bold; text-decoration: none;">]] </del>or a .cel file from the Affy software. These type of data sets are called ''raw data'', as they normally need further processing to be usefull. In the case of a spotted <del style="font-weight: bold; text-decoration: none;">!</del>cDNA microarray these datasets must as a minimum contain the foreground and background intensities for each channel. Location information on the exact spot position is also often required, for instance to draw a false colour image of the microarray with the location of the spots to click on. </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Well, that is just what it says, a set of data, in the special case of EMMA a matrix of numbers. These data might be the output of an external image analysis software like ImaGene, GenePix or a .cel file from the Affy software. These type of data sets are called ''raw data'', as they normally need further processing to be usefull. In the case of a spotted cDNA microarray these datasets must as a minimum contain the foreground and background intensities for each channel. Location information on the exact spot position is also often required, for instance to draw a false colour image of the microarray with the location of the spots to click on. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>While rows of a raw dataset correspond to individual spots on the array, columns correspond to different types of measurments like foreground background and location values. These are called ''<del style="font-weight: bold; text-decoration: none;">[[</del>QuantitationTypes<del style="font-weight: bold; text-decoration: none;">]]</del>''. You think of them as simply being column headers for the matrix.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>While rows of a raw dataset correspond to individual spots on the array, columns correspond to different types of measurments like foreground background and location values. These are called ''QuantitationTypes''. You think of them as simply being column headers for the matrix.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Several analysis methods like for instance ''<del style="font-weight: bold; text-decoration: none;">[[</del>Normalization<del style="font-weight: bold; text-decoration: none;">]]</del>'' will take raw datasets and produce new datasets by computation. These datasets are called ''Transformed Datasets''. In Transformed Datasets often rows do not correspond to individual spots any more but to genes. Of course different ''<del style="font-weight: bold; text-decoration: none;">[[</del>QuantitationTypes<del style="font-weight: bold; text-decoration: none;">]]</del>'' also exist for Derived Datasets. Which <del style="font-weight: bold; text-decoration: none;">[[</del>QuantitationTypes<del style="font-weight: bold; text-decoration: none;">]] </del>are actually there depends on the chosen analysis method.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Several analysis methods like for instance ''Normalization'' will take raw datasets and produce new datasets by computation. These datasets are called ''Transformed Datasets''. In Transformed Datasets often rows do not correspond to individual spots any more but to genes. Of course different ''QuantitationTypes'' also exist for Derived Datasets. Which QuantitationTypes are actually there depends on the chosen analysis method.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Each Dataset has to be assigned to at least one Experiment. Raw Datasets can also belong to sevaral experiments. They are automatically added to an Experiment when the corresponding Arrays are assigned.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Each Dataset has to be assigned to at least one Experiment. Raw Datasets can also belong to sevaral experiments. They are automatically added to an Experiment when the corresponding Arrays are assigned.</div></td></tr>
</table>imported>VirginieMittardhttps://wiki.cebitec.uni-bielefeld.de/brf-software/index.php?title=EMMAWiki/TermsAndConcepts/ForUsers/Datasets&diff=1081&oldid=previmported>MichaelDondrup at 11:46, 19 April 20052005-04-19T11:46:35Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>While rows of a raw dataset correspond to individual spots on the array, columns correspond to different types of measurments like foreground background and location values. These are called ''[[QuantitationTypes]]''. You think of them as simply being column headers for the matrix.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>While rows of a raw dataset correspond to individual spots on the array, columns correspond to different types of measurments like foreground background and location values. These are called ''[[QuantitationTypes]]''. You think of them as simply being column headers for the matrix.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Several analysis methods like for instance ''[[Normalization]]'' will take raw datasets <del style="font-weight: bold; text-decoration: none;">andproduce </del>new datasets by computation. These datasets are called ''Transformed Datasets''. In Transformed Datasets often rows do not correspond to individual spots any more but to genes. Of course different ''[[QuantitationTypes]]'' also exist for Derived Datasets. Which [[QuantitationTypes]] are actually there depends on the chosen analysis method.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Several analysis methods like for instance ''[[Normalization]]'' will take raw datasets <ins style="font-weight: bold; text-decoration: none;">and produce </ins>new datasets by computation. These datasets are called ''Transformed Datasets''. In Transformed Datasets often rows do not correspond to individual spots any more but to genes. Of course different ''[[QuantitationTypes]]'' also exist for Derived Datasets. Which [[QuantitationTypes]] are actually there depends on the chosen analysis method.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Each Dataset has to be assigned to at least one Experiment. Raw Datasets can also belong to sevaral experiments. They are automatically added to an Experiment when the corresponding Arrays are assigned.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Each Dataset has to be assigned to at least one Experiment. Raw Datasets can also belong to sevaral experiments. They are automatically added to an Experiment when the corresponding Arrays are assigned.</div></td></tr>
</table>imported>MichaelDondruphttps://wiki.cebitec.uni-bielefeld.de/brf-software/index.php?title=EMMAWiki/TermsAndConcepts/ForUsers/Datasets&diff=1080&oldid=previmported>MichaelDondrup at 11:46, 19 April 20052005-04-19T11:46:17Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 13:46, 19 April 2005</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Several analysis methods like for instance ''[[Normalization]]'' will take raw datasets andproduce new datasets by computation. These datasets are called ''Transformed Datasets''. In Transformed Datasets often rows do not correspond to individual spots any more but to genes. Of course different ''[[QuantitationTypes]]'' also exist for Derived Datasets. Which [[QuantitationTypes]] are actually there depends on the chosen analysis method.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Several analysis methods like for instance ''[[Normalization]]'' will take raw datasets andproduce new datasets by computation. These datasets are called ''Transformed Datasets''. In Transformed Datasets often rows do not correspond to individual spots any more but to genes. Of course different ''[[QuantitationTypes]]'' also exist for Derived Datasets. Which [[QuantitationTypes]] are actually there depends on the chosen analysis method.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Each Dataset has to be assigned to at least one Experiment. Raw Datasets can also belong to sevaral experiments. They are automatically added to an Experiment when the corresponding Arrays are assigned</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Each Dataset has to be assigned to at least one Experiment. Raw Datasets can also belong to sevaral experiments. They are automatically added to an Experiment when the corresponding Arrays are assigned<ins style="font-weight: bold; text-decoration: none;">.</ins></div></td></tr>
</table>imported>MichaelDondruphttps://wiki.cebitec.uni-bielefeld.de/brf-software/index.php?title=EMMAWiki/TermsAndConcepts/ForUsers/Datasets&diff=1079&oldid=previmported>MichaelDondrup at 11:46, 19 April 20052005-04-19T11:46:05Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 13:46, 19 April 2005</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= Terms and Concepts: Dataset =</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= Terms and Concepts: Dataset =</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Well, that is just what it says, a set of data, in the special case a matrix of numbers. These data might be the output of an external image analysis software like [[ImaGene]], [[GenePix]] or a .cel file from the Affy software. These type of data sets are called ''raw data'', as they normally need further processing to be usefull. In the case of a spotted !cDNA microarray these datasets must as a minimum contain the foreground and background intensities for each channel. Location information on the exact spot position is also often required, for instance to draw a false colour image of the microarray with the location of the spots to click on. </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Well, that is just what it says, a set of data, in the special case <ins style="font-weight: bold; text-decoration: none;">of EMMA </ins>a matrix of numbers. These data might be the output of an external image analysis software like [[ImaGene]], [[GenePix]] or a .cel file from the Affy software. These type of data sets are called ''raw data'', as they normally need further processing to be usefull. In the case of a spotted !cDNA microarray these datasets must as a minimum contain the foreground and background intensities for each channel. Location information on the exact spot position is also often required, for instance to draw a false colour image of the microarray with the location of the spots to click on. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>While rows of a raw dataset correspond to individual spots on the array, columns correspond to different types of measurments like foreground background and location values. These are called ''[[QuantitationTypes]]''. You think of them as simply being column headers for the matrix.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>While rows of a raw dataset correspond to individual spots on the array, columns correspond to different types of measurments like foreground background and location values. These are called ''[[QuantitationTypes]]''. You think of them as simply being column headers for the matrix.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Several analysis methods like for instance ''[[Normalization]]'' will take raw datasets andproduce new datasets by computation. These datasets are called ''Transformed Datasets''. In Transformed Datasets often rows do not correspond to individual spots any more but to genes. Of course different ''[[QuantitationTypes]]'' also exist for Derived Datasets. Which [[QuantitationTypes]] are actually there depends on the chosen analysis method.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Several analysis methods like for instance ''[[Normalization]]'' will take raw datasets andproduce new datasets by computation. These datasets are called ''Transformed Datasets''. In Transformed Datasets often rows do not correspond to individual spots any more but to genes. Of course different ''[[QuantitationTypes]]'' also exist for Derived Datasets. Which [[QuantitationTypes]] are actually there depends on the chosen analysis method.</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Each Dataset has to be assigned to at least one Experiment. Raw Datasets can also belong to sevaral experiments. They are automatically added to an Experiment when the corresponding Arrays are assigned</ins></div></td></tr>
</table>imported>MichaelDondruphttps://wiki.cebitec.uni-bielefeld.de/brf-software/index.php?title=EMMAWiki/TermsAndConcepts/ForUsers/Datasets&diff=1078&oldid=previmported>MichaelDondrup at 10:30, 19 April 20052005-04-19T10:30:36Z<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 12:30, 19 April 2005</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l4">Line 4:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Well, that is just what it says, a set of data, in the special case a matrix of numbers. These data might be the output of an external image analysis software like [[ImaGene]], [[GenePix]] or a .cel file from the Affy software. These type of data sets are called ''raw data'', as they normally need further processing to be usefull. In the case of a spotted !cDNA microarray these datasets must as a minimum contain the foreground and background intensities for each channel. Location information on the exact spot position is also often required, for instance to draw a false colour image of the microarray with the location of the spots to click on. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>Well, that is just what it says, a set of data, in the special case a matrix of numbers. These data might be the output of an external image analysis software like [[ImaGene]], [[GenePix]] or a .cel file from the Affy software. These type of data sets are called ''raw data'', as they normally need further processing to be usefull. In the case of a spotted !cDNA microarray these datasets must as a minimum contain the foreground and background intensities for each channel. Location information on the exact spot position is also often required, for instance to draw a false colour image of the microarray with the location of the spots to click on. </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>While rows of a raw dataset correspond to individual spots on the array, columns correspond to different types of measurments like foreground background and location values. These are called ''[[QuantitationTypes]]''.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>While rows of a raw dataset correspond to individual spots on the array, columns correspond to different types of measurments like foreground background and location values. These are called ''[[QuantitationTypes]]''<ins style="font-weight: bold; text-decoration: none;">. You think of them as simply being column headers for the matrix</ins>.</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Several analysis methods like for instance ''[[Normalization]]'' will take raw datasets andproduce new datasets by computation. These datasets are called ''Transformed Datasets''. In Transformed Datasets often rows do not correspond to individual spots any more but to genes. Of course different ''[[QuantitationTypes]]'' also exist for Derived Datasets. Which <del style="font-weight: bold; text-decoration: none;">Quantitationtypes </del>are actually <del style="font-weight: bold; text-decoration: none;">used </del>depends on the chosen analysis method.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Several analysis methods like for instance ''[[Normalization]]'' will take raw datasets andproduce new datasets by computation. These datasets are called ''Transformed Datasets''. In Transformed Datasets often rows do not correspond to individual spots any more but to genes. Of course different ''[[QuantitationTypes]]'' also exist for Derived Datasets. Which <ins style="font-weight: bold; text-decoration: none;">[[QuantitationTypes]] </ins>are actually <ins style="font-weight: bold; text-decoration: none;">there </ins>depends on the chosen analysis method.</div></td></tr>
</table>imported>MichaelDondruphttps://wiki.cebitec.uni-bielefeld.de/brf-software/index.php?title=EMMAWiki/TermsAndConcepts/ForUsers/Datasets&diff=1077&oldid=previmported>MichaelDondrup at 10:29, 19 April 20052005-04-19T10:29:06Z<p></p>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= Terms and Concepts: Dataset =</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>= Terms and Concepts: Dataset =</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Well, that is just what it says, a set of data, in the special case a matrix of numbers. These data might be the output of an external image analysis software like [[ImaGene]], [[GenePix]] or a .cel file from the Affy software. These type of data sets are called ''raw data'', as they normally need further processing to</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Well, that is just what it says, a set of data, in the special case a matrix of numbers. These data might be the output of an external image analysis software like [[ImaGene]], [[GenePix]] or a .cel file from the Affy software. These type of data sets are called ''raw data'', as they normally need further processing to <ins style="font-weight: bold; text-decoration: none;">be usefull. In the case of a spotted !cDNA microarray these datasets must as a minimum contain the foreground and background intensities for each channel. Location information on the exact spot position is also often required, for instance to draw a false colour image of the microarray with the location of the spots to click on. </ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">While rows of a raw dataset correspond to individual spots on the array, columns correspond to different types of measurments like foreground background and location values. These are called ''[[QuantitationTypes]]''.</ins></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">Several analysis methods like for instance ''[[Normalization]]'' will take raw datasets andproduce new datasets by computation. These datasets are called ''Transformed Datasets''. In Transformed Datasets often rows do not correspond to individual spots any more but to genes. Of course different ''[[QuantitationTypes]]'' also exist for Derived Datasets. Which Quantitationtypes are actually used depends on the chosen analysis method.</ins></div></td></tr>
</table>imported>MichaelDondruphttps://wiki.cebitec.uni-bielefeld.de/brf-software/index.php?title=EMMAWiki/TermsAndConcepts/ForUsers/Datasets&diff=1075&oldid=previmported>MichaelDondrup at 10:10, 19 April 20052005-04-19T10:10:15Z<p></p>
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