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Old 03-24-2014, 01:06 PM   #1
rajarapupriya
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Default Changing FDR in DESeq2

Could anyone please tell me how to change the FDR from default (0.1) to 0.05 in DESeq2.

Thanks
Priya
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Old 03-26-2014, 08:38 PM   #2
Jeremy
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at which step?
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Old 03-27-2014, 08:36 AM   #3
rajarapupriya
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Thanks Jeremy for replying to my question. I would like to change FDR before/while calculating the differential gene expression. I'm using DESeq2 1.2.10 Vignette. The entire differential expression steps are distilled to one step DESeq(). That is where I'm having problem.

Priya
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Old 03-27-2014, 01:43 PM   #4
Michael Love
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You can choose whatever adjusted p-value cutoff you like after DESeq() and results(). DESeq() does not perform multiple test correction.

dds <- DESeq(dds)
res <- results(dds)
resSig <- res[which(res$padj < 0.05),]

The independent filtering in results() has an argument 'alpha', which is used to optimize a cutoff on mean normalized count, to maximize the number of genes with padj < alpha.

So you can do:

res <- results(dds, alpha=.05)
resSig <- res[which(res$padj < 0.05),]

Lots of useful information in ?DESeq and ?results.
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Old 03-27-2014, 01:59 PM   #5
rajarapupriya
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Thanks, Michael !! Think I missed it somewhere.

Priya
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Old 03-28-2014, 12:27 AM   #6
Jeremy
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The object res has the results for all of the genes and their FDR adjusted p-values. I always just merge res with the corrected count data and then write it all out to a tab delimited table then you have all the information that you can put in as a supplementary file.
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Old 03-28-2014, 08:21 AM   #7
rajarapupriya
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Thank you, Jeremy !!
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