Lenaolufson Week 15

12/8/15

• It was now time for me to prepare my file for GenMAPP, and I did so by the Vibrio cholerae instructions found here.]
• I inserted a new worksheet and named it "forGenMAPP".
• I went back to the "statistics" worksheet and Selected All and Copied.
• I went to my new sheet and clicked on cell A1 and selected Paste Special, clicked on the Values radio button, and clicked OK.
  • I then deleted the ID columns besides the far left one in column A, and I deleted the second MasterIndex column because it was unnecessary.
  • I added a "1" before all of the titles of columns D through I so that none of the columns would have the same names due to the replicates.
• I selected Columns V through Y (all the fold changes). I selected the menu item Format > Cells. Under the number tab, I selected 2 decimal places. I clicked OK.
• I selected all the columns containing p values. I selected the menu item Format > Cells. Under the number tab, I selected 4 decimal places. I clicked OK.
• I deleted the left-most Bonferroni p value column, preserving the one that showed the result of my "if" statement.
• I inserted a column to the right of the "ID" column. I typed the header "SystemCode" into the top cell of this column. I filled the entire column (each cell) with the letter "N".
• I selected the menu item File > Save As, and chose "Text (Tab-delimited) (*.txt)" from the file type drop-down menu.
• After preparing it for GenMAPP, here are the .xls and .txt files:
  • File:Bpertussis CompiledRawData MS2015-3.xlsx
  • File:Bpertussis CompiledRawData MS2015-3.txt

• p-value less than 0.05: 1923/3552
• p-value less than 0.01: 1028/3552
• p-value less than 0.001: 242/3552
• p-value less than 0.0001: 40/3552
• p < 0.05 for the Bonferroni-corrected p value: 9/3552
• p < 0.05 for the Benjamini and Hochberg-corrected p value: 1365/3552File:Gene ontology results.png
• Keeping the (unadjusted) "Pvalue" filter at p < 0.05, filter the "Avg_LogFC_all" column to show all genes with an average log fold change greater than zero. How many are there?
  • 964/3552
• Keeping the (unadjusted) "Pvalue" filter at p < 0.05, filter the "Avg_LogFC_all" column to show all genes with an average log fold change less than zero. How many are there?
  • 959/3552
• What about an average log fold change of > 0.25 and p < 0.05?
  • 874/3552
• Or an average log fold change of < -0.25 and p < 0.05?
  • 848/3552
• the fold change cut-off of greater than 0.25 or less than -0.25 and the unadjusted p value cut off of p < 0.05?
  • 1722/3552
• numbers of errors found when running the .txt file in the GenMAPP database: 342 errors
• 23 replacements for the #DIV/0!
  • 339 errors with new .txt file
• links to files created:
  • File:Bpertussis CompiledRawData MS2015-3.EX.txt
  • File:Bpertussis CompiledRawData MS2015-3.xlsx
  • File:Bpertussis CompiledRawData MS2015-3.txt
  • File:Bpertussis CompiledRawData MS2015-3.gex
  • Media:MAPPFinder results for geneontologyresultsCriterion1-GOtxt.png
  • Media:Gene ontology results.png
  • Media:Errors in GenMAPP.png