https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?action=history&feed=atom&title=Week_12_E-notes_EyanoschWeek 12 E-notes Eyanosch - Revision history2026-04-08T16:40:17ZRevision history for this page on the wikiMediaWiki 1.25.1https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?title=Week_12_E-notes_Eyanosch&diff=6717&oldid=prevEyanosch: added a link to the OTS files downloaded to the wiki and edited the dye section of the week 12 notes2015-11-23T01:22:55Z<p>added a link to the OTS files downloaded to the wiki and edited the dye section of the week 12 notes</p>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 01:22, 23 November 2015</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Downloaded the "raw" data and the "sdrf.txt" data</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Downloaded the "raw" data and the "sdrf.txt" data</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; 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>Found that the experimental design did not involve dyeswaps the control was the Cy3 dye throughout the whole experiment</div></td><td class='diff-marker'>+</td><td style="color:black; 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>Found that the experimental design did not involve dyeswaps the control was the Cy3 <ins class="diffchange diffchange-inline">dye and treatments the Cy5 </ins>dye throughout the whole experiment<ins class="diffchange diffchange-inline">.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Downloaded 36 sdrf.txt files each file holds data for a certain time point in the experiment for both the drug and control hybridized.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>Downloaded 36 sdrf.txt files each file holds data for a certain time point in the experiment for both the drug and control hybridized.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>ex. -> Rx 0.5 MIC and control at time 10 with the replicate number</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>ex. -> Rx 0.5 MIC and control at time 10 with the replicate number</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>We will use the shorthand for each ID column taken from the gpr files that corresponds with the raw data.</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>We will use the shorthand for each ID column taken from the gpr files that corresponds with the raw data.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; 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> </div></td><td class='diff-marker'>+</td><td style="color:black; 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 class="diffchange diffchange-inline">We then combined all files into one master data file by copying/pasting the spreadsheets into one document and uploaded it to the team's file page found [[OTS Files | here]]</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; 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>[[Category: Journal Entry, Week <del class="diffchange diffchange-inline">10 </del>Journal Entry]]</div></td><td class='diff-marker'>+</td><td style="color:black; 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>[[Category: Journal Entry, Week <ins class="diffchange diffchange-inline">12 </ins>Journal Entry]]</div></td></tr>
</table>Eyanoschhttps://xmlpipedb.lmucs.io/biodb/fall2015/index.php?title=Week_12_E-notes_Eyanosch&diff=6573&oldid=prevEyanosch: adding the process2015-11-20T00:17:34Z<p>adding the process</p>
<p><b>New page</b></p><div><br />
User Page: [[User: Eyanosch | Erich Yanoschik]]<br />
Team Page: [[Team_4 | Oregon Trail Survivors]]<br />
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Downloaded the "raw" data and the "sdrf.txt" data<br />
Found that the experimental design did not involve dyeswaps the control was the Cy3 dye throughout the whole experiment<br />
Downloaded 36 sdrf.txt files each file holds data for a certain time point in the experiment for both the drug and control hybridized.<br />
ex. -> Rx 0.5 MIC and control at time 10 with the replicate number<br />
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shorthand -> RX 0.5-10-1<br />
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What we are going to do now is order the data in a way that makes sense, taking the ID and Log ratio from the .gpr files<br />
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We will use the shorthand for each ID column taken from the gpr files that corresponds with the raw data.<br />
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{{Template: Pertinent Class Information}}<br />
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[[Category: Journal Entry, Week 10 Journal Entry]]</div>Eyanosch