Changing FDR in DESeq2

[rajarapupriya]

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

Thanks
Priya

[Jeremy]

at which step?

[rajarapupriya]

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

[Michael Love]

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.

[rajarapupriya]

Thanks, Michael !! Think I missed it somewhere.

Priya

[Jeremy]

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.

[rajarapupriya]

Thank you, Jeremy !!