[BioC] DEXSeq output table

Mariana [guest] guest at bioconductor.org
Mon Jun 24 02:26:50 CEST 2013


I've used the DESeq package and now I'm trying the DEXSeq one.

In the DESeq package I can access the baseMean, baseMeanA, baseMeanB values before doing the analysis, but using the DEXSeq package, I only get the meanBase value.

How can I get the baseMeanA baseMeanB values using the DEXSeq package?




 -- output of sessionInfo(): 

> head(res1)
                                              geneID exonID   dispersion pvalue padjust     meanBase
rajko.90nt.slRNA-3.1.1:E001   rajko.90nt.slRNA-3.1.1   E001 1.760727e-02     NA      NA 152.07637815
rajko.90nt.slRNA-31.1.1:E001 rajko.90nt.slRNA-31.1.1   E001 6.178367e-02     NA      NA  19.12018340
rajko.90nt.slRNA-39.1.1:E001 rajko.90nt.slRNA-39.1.1   E001 5.967594e-02     NA      NA  19.95246225
rajko.90nt.slRNA-41.1.1:E001 rajko.90nt.slRNA-41.1.1   E001 1.668097e+01     NA      NA   0.05795718
rajko.90nt.slRNA-45.1.1:E001 rajko.90nt.slRNA-45.1.1   E001 1.000000e+08     NA      NA   0.00000000
rajko.90nt.slRNA-46.1.1:E001 rajko.90nt.slRNA-46.1.1   E001 6.830553e-01     NA      NA   1.43811945
rajko.90nt.slRNA-3.1.1:E001                NA
rajko.90nt.slRNA-31.1.1:E001               NA
rajko.90nt.slRNA-39.1.1:E001               NA
rajko.90nt.slRNA-41.1.1:E001               NA
rajko.90nt.slRNA-45.1.1:E001               NA
rajko.90nt.slRNA-46.1.1:E001               NA

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