Difference between revisions of "Lenaolufson Week 15"
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==12/8/15== | ==12/8/15== | ||
| + | *It was now time for me to prepare my file for GenMAPP, and I did so by the [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae ''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: | *After preparing it for GenMAPP, here are the .xls and .txt files: | ||
** [[File:Bpertussis CompiledRawData MS2015-3.xlsx]] | ** [[File:Bpertussis CompiledRawData MS2015-3.xlsx]] | ||
** [[File:Bpertussis CompiledRawData MS2015-3.txt]] | ** [[File:Bpertussis CompiledRawData MS2015-3.txt]] | ||
| + | |||
*p-value less than 0.05: 1923/3552 | *p-value less than 0.05: 1923/3552 | ||
*p-value less than 0.01: 1028/3552 | *p-value less than 0.01: 1028/3552 | ||
Revision as of 21:19, 10 December 2015
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:
- 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
