[Bioc-sig-seq] Adjusted p values in edgeR

[Davis McCarthy]

Sara

In edgeR if you call 
top <- topTags(d, n=Inf)
then you will get FDR (or whatever adjustment method you like, see argument adjust.method for topTags()) for each gene. 

In general, if you have a vector of p-values then you can use the p.adjust() function to get adjusted p-values---FDR is one of several options. This is precisely the function used by edgeR to compute adjusted p-values to control FDR. See ?p.adjust.

Cheers
Davis


On Jul 1, 2011, at 5:34 AM, Garg, Kavita wrote:

> 
> The output of topTags has that information
> top = topTags(d, n = 500)
> top$table has a adj.P.Val column
> 
> ----- Original Message -----
> From: "Sara Hanson" <sarahanson5 at gmail.com>
> To: bioc-sig-sequencing at r-project.org
> Sent: Thursday, June 30, 2011 12:22:44 PM
> Subject: [Bioc-sig-seq] Adjusted p values in edgeR
> 
> I am analyzing differential expression with next gen sequencing data. I have
> successfully gotten an output from the program containing the p-values
> calculated for each gene, but I am not sure how to output the p-values
> adjusted using the FDR method. From the edgeR manual, I can get a summary of
> the number of genes that are significantly differentially expressed based on
> adjusted p-values, but I do not know how to output the actual list of
> adjusted p-values for my dataset. Can anyone help me with this?
> 
> I apologize if this question is naive, but I am a novice with R. Thanks in
> advance!
> 
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------------------------------------------------------------------------
Davis J McCarthy
Research Technician
Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville, Vic 3052, Australia
dmccarthy at wehi.edu.au
http://www.wehi.edu.au




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