https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?action=history&feed=atom&title=Kmeilak_Week_14Kmeilak Week 14 - Revision history2026-06-02T22:57:35ZRevision history for this page on the wikiMediaWiki 1.20.3https://xmlpipedb.lmucs.io/biodb/fall2013/index.php?title=Kmeilak_Week_14&diff=6706&oldid=prevKmeilak at 18:17, 5 December 20132013-12-05T18:17:14Z<p></p>
<table class='diff diff-contentalign-left'>
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 18:17, 5 December 2013</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 8:</td>
<td colspan="2" class="diff-lineno">Line 8:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This page has been written with the analysis of the ''Vibrio cholerae'' dataset in mind.  However, these steps are similar to what needs to be performed with ''any'' microarray dataset (see [[BIOL398-01/S10:DNA_Microarrays#Overview_of_Microarray_Data_Analysis | Overview of Microarray Data Analysis]], although the details will differ with the particular experimental design.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This page has been written with the analysis of the ''Vibrio cholerae'' dataset in mind.  However, these steps are similar to what needs to be performed with ''any'' microarray dataset (see [[BIOL398-01/S10:DNA_Microarrays#Overview_of_Microarray_Data_Analysis | Overview of Microarray Data Analysis]], although the details will differ with the particular experimental design.</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">== Before we begin... ==</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">* The data from the Merrell et al. (2002) paper was accessed from [http://smd.princeton.edu/cgi-bin/publication/viewPublication.pl?pub_no=119 this page] at the Stanford Microarray Database (now hosted by Princeton ''&mdash; [[User:Kam D. Dahlquist|Kam D. Dahlquist]] 18:26, 7 October 2013 (EDT)''.</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">* The Log<sub>2</sub> of R/G Normalized Ratio (Median) has been copied from the raw data files downloaded from the Stanford Microarray Database.</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">**'''Patient A'''</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">***Sample 1: 24047.xls (A1)</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">***Sample 2: 24048.xls (A2)</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">***Sample 3: 24213.xls (A3)</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">***Sample 4: 24202.xls (A4)</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">**'''Patient B'''</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">***Sample 5: 24049.xls (B1)</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">***Sample 6: 24050.xls (B2)</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">***Sample 7: 24203.xls (B3)</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">***Sample 8: 24204.xls (B4)</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">**'''Patient C'''</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">***Sample 9: 24053.xls (C1)</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">***Sample 10: 24054.xls (C2)</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">***Sample 11: 24205.xls (C3)</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">***Sample 12: 24206.xls (C4)</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">**'''Stationary Samples''' (We will not be using these, they are listed here for completeness, but do not appear in your compiled raw data file.)</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">***Sample 13: 24059.xls (Stationary-1)</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">***Sample 14: 24060.xls (Stationary-2)</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">***Sample 15: 24211.xls (Stationary-3)</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">***Sample 16: 24212.xls (Stationary-4)</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">* Download the [[Media:Merrell_Compiled_Raw_Data_Vibrio.xls | Merrell_Compiled_Raw_Data_Vibrio.xls]] file to your Desktop.</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">** Save a copy of the file with a different filename that includes your initials and the date.  For example, I would call mine "Merrell_Compiled_Raw_Data_Vibrio_KD_20091020.xls".</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Normalize the log ratios for the set of slides in the experiment ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Normalize the log ratios for the set of slides in the experiment ==</div></td></tr>
</table>Kmeilak