Dahlquist:Notebook/Nutrigenomics/2010/02/22

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2/22/10

GenMAPP Day 1

  • Followed GenMAPP protocol from the Bioinformatics Wiki page from 2008
  • Formatted my Excel sheet in order to make it compatible to run with GenMAPP
  • Added in the Gene ID's from Afymetrix and inserted a column next to it where I put the letter X down the entire colunmn for the System ID
  • Saved this as a txt file with the gene ids, system ID, the p-values and the log Fold Changes
  • input the data into GenMAPP and ran to see how many errors
  • 3431 errors were found
  • Removed 208 genes that contained nonnumerical values and re-ran the data in GenMAPP
  • After second run through there were 3276 errors