User:Kam D. Dahlquist/Notebook/Personal/2010/11/04

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Re-Do of Andrew's Data Analysis

  • Checked GenePix Pro Manual to verify that results are saved as "Normalized" before I begin.
  • Compiled the "Log Ratio (635/532)", column AS, from each of the individual .gpr results files into a single spreadsheet.
    • The list of chips and their provenance can be found in the "MicroarrayLog.xls" file.
    • The name of the data file is "deltaGLN3_microarray_data_processed_20101104_KD.xls"
    • Name of the worksheet is "compiledrawdata"
    • The column headers are named according to "barcode_F#_tX" where F# is the flask number, tX is the timepoint, and there is an optional "_swapped" if the dye orientation of the t0 was red instead of green.
  • Corrected all chips to have the same dye orientation of t0 being green in the denominator.
    • Name of sheet is "correctdyeorientation"
    • Multiplied the appropriate columns by -1, removed the "_swapped" from the column header, and pasted over with paste values.
  • Note: at this point, departed from previous method of doing the analysis. Removed all control spots, ones designated "3XSSC" or "Arabidopsis", pasted into new sheet "removedcontrolspots". total of 620 rows removed
    • Replaced all cells with "Error" (1526 replacements) or "#VALUE!" contents with a single space character (876 replacements).
    • Saved As "deltaGLN3_microarray_data_processed_20101104_KD_formatlab.xls" and deleted all sheets except for "removedcontrolspots".
  • Ran matlab script "splitting_kams_file.m" on this Excel file which created two new files with "_odd" and "_even" appended to the filename.
    • For some reason, the IDs in the "odd" file are off, need to be shifted up by one and the last row needs to have the ID copied from the original file.
  • Pasted results of _odd and _even files into master spreadsheet into worksheet called "Avg_odd_even_rows"
    • Averaged the odd and even rows.
  • Pasted results (paste values) into new sheet "BetweenChipNorm"
    • replaced all "#DIV/0!" with single space character (518 replacements)
  • Scaled and centered values by subtracting the mean and dividing by the standard deviation
  • Paste scaled and centered values (not formulas) into new sheet called "statistics"
    • replace all "#VALUE!" with single space character (518 replacements)
  • Calculate average log fold changes, TSTAT and P value. Format for GenMAPP and Run MAPPFinder.

To Do