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

From OpenWetWare
Jump to: navigation, search

HeaderBlueBig.gif Home        Research        Protocols        Notebook        People        Publications        Courses        Contact       


Owwnotebook icon.png Microarray Data Analysis Report.pngMain project page
Resultset previous.pngPrevious entry      Next entryResultset next.png

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)