Dahlquist:Notebook/Nutrigenomics/2009/11/19

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 * style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]] Nutrigenomics
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 * style="background-color: #F2F2F2" align="center"|  |Main project page


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Stephen

 * Table of Mice in Paper vs. Mice on Disk

Dr. Dahlquist

 * Stephen was unable to load his files last week into dChip, so I am going to try and see if I can do it.
 * Opened file <1_12 wk_TRAMP.CEL> with Excel (did not completely load) to check the version number of the Affy chip.
 * Chip verion is MOE430A.1sq
 * Verified that all .CEL files had same chip version
 * noticed that the 18th line of the file did not load properly into Excel and was showing the box tab characters
 * Affy Site for this chip
 * Downloaded , shown as Library Files > Mouse Expression Set 430 (zip, 24 MB) on the Affy site.
 * Unzipped with 7-zip. The actual CDF file is found in CD_MOE430\Full\MOE430A\LibFiles\MOE430A.CDF.  Copied it and moved it to the higher directory with the data.
 * Launched dChip (Build date: Jul 13 2009)
 * Chose menu item Analysis > Open Group
 * Called group "dChip"
 * Chose file directory with .CEL files
 * Said that suffix of TXT/CHP file was .CEL
 * Under Other information tab, selected MOE430A.CDF file
 * Clicked OK and got the [[Media:DChip_log_20091119.txt | following messages]].
 * Data appeared to load correctly and create a .dcp file for each .CEL file.
 * Stephen verified that a "Group" should be all of the chips in the experiment by reading the manual.


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