Dahlquist:Notebook/Microarray Data Analysis/2008/10/29

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


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Adding Edge statistics to Master microarray data file
E:\Lab Records\Students\Entzminger_Kevin\EdgeAnalysis_20081021 E:\Lab Records\Microarray Data Analysis 20080630\wt-dCIN5_consolidated_genesymbols-CIN5targets-added_20080702.xls E:\Lab Records\Microarray Data Analysis 20081029
 * Kevin's Edge data is stored in
 * See 2008-20-21 Notebook Entry for how these files were generated.
 * There are three Edge results files:
 * GeneList_20081014_wt-only.txt
 * GeneList_20081021_dCIN5-only.txt
 * GeneList_20081021_wt-vs-dCIN5.txt
 * The Edge data files have four columns:
 * Rank
 * Gene Name (we used our Gene Index for this)
 * P-value
 * Q-value
 * Will change these column names to add comparison for clarity in Master spreadsheet. Appended "_edited_20081029-KD" to each filename when I made this change.
 * The Master spreadsheet I will be adding to is:
 * I copied it into a new folder
 * Exported the "fromAccess" worksheet as a tab-delmitted text file named "wt-dCIN5_consolidated.txt. Access wouldn't let me import a .txt file with a filename longer than 64 characters.
 * Had the change the data type for the index in the Edge files from text to number to perform the queries.
 * Query1 merges wt-only with consolidated data.
 * Query2 merges dCIN5-only with query above.
 * Query3 merges wt-vs-dCIN5 with query above creating table "consolidated-all"
 * To take the data back to Excel, can't export as text because it will cut off the significant digits in the data, but exporting it as a .xls is OK. Called the file "wt-dCIN5-consolidated-Edge_20081029.xls"
 * Upon examining the merged data in Excel, it looks like something is wrong. There are 252 blank records for the dCIN5-only data columns, but those records have expression data for those genes for dCIN5.  I am thinking that the gene index got messed up for the dCIN5-only data run in Edge and will have to be redone.  I need to talk to Kevin about this.

&mdash; Kam D. Dahlquist 21:10, 29 October 2008 (EDT)


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