I used DESeq2 and found it report more deferentially expressed genes than before. Actually, it is not reasonable.
I noticed the
padj column is different from the values I am calculating using the p.adjust (pvalue column). I would like you to tell me the incorrect of my calculation, or some bugs in DESeq2. Thanks a lot. In the following, I pasted my sessionInfo()
> sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-unknown-linux-gnu (64-bit) locale:  C attached base packages:  splines parallel stats graphics grDevices utils datasets  methods base other attached packages:  cqn_1.10.0 quantreg_5.05 SparseM_1.05  preprocessCore_1.26.1 nor1mix_1.2-0 mclust_4.3  DESeq2_1.4.5 RcppArmadillo_0.4.400.0 Rcpp_0.11.2  GenomicRanges_1.16.4 GenomeInfoDb_1.0.2 IRanges_1.22.10  BiocGenerics_0.10.0 loaded via a namespace (and not attached):  AnnotationDbi_1.26.0 Biobase_2.24.0 DBI_0.3.0  RColorBrewer_1.0-5 RSQLite_0.11.4 XML_3.98-1.1  XVector_0.4.0 annotate_1.42.1 genefilter_1.46.1  geneplotter_1.42.0 grid_3.1.0 lattice_0.20-29  locfit_1.5-9.1 stats4_3.1.0 survival_2.37-7  xtable_1.7-4