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

Garg, Kavita kgarg at fhcrc.org
Thu Jun 30 21:34:18 CEST 2011

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

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