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Old 11-07-2012, 10:34 PM   #1
gene_x
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Default 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!
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Old 11-08-2012, 12:26 AM   #2
NicoBxl
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In every stat book.
Here an example : http://udel.edu/~mcdonald/statmultcomp.html
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Old 11-08-2012, 05:33 PM   #3
gene_x
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thanks for the reply.. but there is no demo in that link of how to calculate it..
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Old 11-08-2012, 11:35 PM   #4
dariober
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Quote:
Originally Posted by gene_x View Post
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
padj<- p.adjust(pvals$V1, method= 'fdr') ## Adjust
write.table(padj, 'pvals.fdr.txt', row.names= FALSE, col.names= FALSE) ## Write to file the corrected pvalues
Hope this helps!
Dario
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Old 11-08-2012, 11:51 PM   #5
gene_x
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thanks, i'll take a look at that in R!
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