[BioC] DESeq multi-factor export results

[Simon Anders]

Hi Ingrid

On 03/21/2012 04:08 PM, Ingrid Lindquist wrote:
> See below. If I'm not mistaken the padjGLM file has the adjusted pvals
> in the order that is in fit1, so I've been manually combining them. Let
> me know though if this is not the correct assumption..

Yes, this is correct.

You can also combine the results into a data frame:

> write.table(fit1, file="fit_c_ctrl")
> write.table(padjGLM, file="padjGLM_c_ctrl")

becomes

write.table(
    data.frame(
       geneID = row.names(counts(cds)),
       pval = pvalsGLM,
       padj = padjGLM,
       fit1 ),
    file = "result.txt" )


   Simon