To the developers,

I'm using DESeq2 version 1.14.1, and I want to upgrade to version 1.16.1, but I'm still stuck with version 1.14.1 I'm using R version 3.3.2 and Bioconductor version 3.4 (BiocInstaller 1.24.0). I tried doing the typical installation in R through the Bioconductor page, but to no avail, I can't get the version 1.16.1.

Also, you mentioned on one of the threads that " "lfcShrink() gives the identical moderated LFCs as DESeq() gave in previous versions." and "If  you want to obtain (nearly) the same results in version 1.16 as in 1.14 you can do: dds <- DESeq(dds, betaPrior=TRUE)." So when running version 1.14.1 using dds <- DESeq(dds, betaPrior=TRUE) would be (nearly) the same when using the lfcShrink of version 1.16.1?

I think the default for version 1.14.1 is dds <- DESeq(dds, betaPrior=TRUE) right? As it is stated on the R documentation that "A zero-centered Normal prior distribution is assumed for the coefficients other than the intercept ."

Please and kindly advise.

Thanks and best regards.

Sincerely,

Asher

Bioconductor packages are tightly linked with the R version. If you want a newer version of DESeq2, you also need to upgrade your version of R.