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

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Today's Workflow

Adding Edge statistics to Master microarray data file

  • Kevin's Edge data is stored in
E:\Lab Records\Students\Entzminger_Kevin\EdgeAnalysis_20081021
  • 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:
E:\Lab Records\Microarray Data Analysis 20080630\wt-dCIN5_consolidated_genesymbols-CIN5targets-added_20080702.xls
  • I copied it into a new folder
E:\Lab Records\Microarray Data Analysis 20081029
  • 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.

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