[BioC] DEXSeq output table
Mariana [guest]
guest at bioconductor.org
Mon Jun 24 02:26:50 CEST 2013
Hi!
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?
Thanks!
[]s
Mariana
-- 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
log2fold(all/sl)
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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