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 11-07-2012, 10:34 PM #1 gene_x Senior Member   Location: MO Join Date: May 2010 Posts: 108 multiple testing correction question in bioinformatics, you'll probably run into the multiple testing correction problem at some time of the analysis.. I have read several places online, including a nature biotech primer, etc, I can understand the basic knowledge behind it but I still don't know how to use it in my research or real-life work.. my understanding is I can compute P-values and then either Bonferroni adjustment or FDR based q-value or so although i don't know how to do so.. Do you know of a tutorial type documents that can explain in detail with examples of how this is done? Thanks so much!
 11-08-2012, 12:26 AM #2 NicoBxl not just another member   Location: Belgium Join Date: Aug 2010 Posts: 264 In every stat book. Here an example : http://udel.edu/~mcdonald/statmultcomp.html
 11-08-2012, 05:33 PM #3 gene_x Senior Member   Location: MO Join Date: May 2010 Posts: 108 thanks for the reply.. but there is no demo in that link of how to calculate it..
11-08-2012, 11:35 PM   #4
dariober
Senior Member

Location: Cambridge, UK

Join Date: May 2010
Posts: 311

Quote:
 Originally Posted by gene_x thanks for the reply.. but there is no demo in that link of how to calculate it..
In practice, this can be done in R with p.adjust. Say pvals.txt is a plain text file with a list of pvalues, one per row (that is, a table with one column):
Code:
```cat pvals.txt
0.1
0.2
0.3
0.4
0.5
0.6
0.7```
In R:

Code:
```pvals<- read.table('pvals.txt') ## Read file with pvalues
write.table(padj, 'pvals.fdr.txt', row.names= FALSE, col.names= FALSE) ## Write to file the corrected pvalues```
Hope this helps!
Dario

 11-08-2012, 11:51 PM #5 gene_x Senior Member   Location: MO Join Date: May 2010 Posts: 108 thanks, i'll take a look at that in R!

 Tags beginner, fdr, multiple testing, statistics