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Old 01-27-2014, 10:25 AM   #21
Location: Mc Gill -- Montreal

Join Date: Dec 2013
Posts: 37

p value is just a widely used joke. The signification of p value is hard to get and imply assumptions that lot of people don t know.
FDR is just a bigger joke. Your best pvalue will most of the time be multiply by your number of p value.
So if you have 10 genes to test giving you 10 pvalues, the best is multiply by 10, the second best by 5, then by 3.3333, then by 2.5, then by 2 etc .....

Here is the code in R

# produce a vector of FDR with an ordered pval vector
fdr = function(pval){
 if(size<2) return(pval)

 #the worst pval is multiply by (size) / (size-1)
 FDR=c( min( 1 , pval[size]*(size)/(size-1)   ))

 for( i in 1:(size-1)) FDR=c(FDR,min(FDR[i] , pval[size-i]*(size)/(size-i)))

 # We have to revers the vector to be consistant
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Old 01-27-2014, 11:39 AM   #22
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Location: Santa Fe, NM

Join Date: Oct 2010
Posts: 250

Originally Posted by Simon Anders View Post
So, what do you suggest to do instead?
I don't know for sure. I first noticed the problem doing some meta-analysis hypothesis testing on coverage merging p-values of bases with each base having a different statistical power. Using Fishers meta-analysis procedure, it became obvious that the underpowered bases were dominating the the test and that Fishers test assumed all published results were adequately powered. It would be nice if that theory were also better. I came up with a heuristic involving weighted sums of -log(p-values) and information entropy as degrees of freedom, which has a certain appeal to it.
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Old 01-27-2014, 12:09 PM   #23
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Location: Norway

Join Date: Aug 2013
Posts: 266

Originally Posted by dpryan View Post
See the "genefilter" package for some useful functions.
Interesting, thanks!
Another question, excuse my ignorance.. But look at these codes:

> FDR <- p.adjust(lrt$table$PValue, method="BH")
> sum(FDR < 0.05)

Is this the way to choose FDR < 0.1:

> FDR <- p.adjust(lrt$table$PValue, method="BH")
> sum(FDR < 0.1)
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Old 02-07-2014, 08:58 AM   #24
Location: Nebraska

Join Date: Oct 2011
Posts: 25

Originally Posted by swbarnes2 View Post
I feel that this is an appropriate contribution:
oh it's so appropriate
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