[BioC] DESeq2

[Shobana Sekar [guest]]

Hi,

I've been using the DESeq as well as DESeq2 packages for my RNAseq analysis. For one particular study alone, I find some discrepancies between DESeq and DESeq2 results. I've read in forums that the gene list is longer when we use DESeq2, which is true in my case. But what I also notice for this study is that there is no overlap between the gene list obtained using DESeq and DESeq2. Could you please help in understanding this difference?

 -- output of sessionInfo(): 

R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] DESeq2_1.2.8          RcppArmadillo_0.4.000 Rcpp_0.10.6           GenomicRanges_1.14.4 
[5] XVector_0.2.0         IRanges_1.20.6        BiocGenerics_0.8.0   


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