Difference between revisions of "Lenaolufson Week 15"
From LMU BioDB 2015
Lenaolufson (Talk | contribs) (added sanity check results) |
Lenaolufson (Talk | contribs) (→12/8/15: added links to files and images) |
||
| Line 8: | Line 8: | ||
*p-value less than 0.0001: 40/3552 | *p-value less than 0.0001: 40/3552 | ||
*p < 0.05 for the Bonferroni-corrected p value: 9/3552 | *p < 0.05 for the Bonferroni-corrected p value: 9/3552 | ||
| − | *p < 0.05 for the Benjamini and Hochberg-corrected p value: 1365/ | + | *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? | *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 | **964/3552 | ||
| Line 19: | Line 19: | ||
* 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? | * 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 | **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]] | ||
Revision as of 00:20, 9 December 2015
12/8/15
- 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
