Question: using DESeq2 v 1.18 in Bioconductor v. 3.8
0
gravatar for gtechbio
26 days ago by
gtechbio0
gtechbio0 wrote:

How can one use DESeq2 v. 1.18 from the latest Bioconductor v. 3.8?

I need to use one package that works reliably only in Bioconductor 3.8, but all my previous analysis was done using DESeq2 v. 1.18, which is from older Bioconductor release. Thanks

deseq2 bioconductor • 77 views
ADD COMMENTlink modified 26 days ago by shepherl ♦♦ 1.3k • written 26 days ago by gtechbio0
Answer: using DESeq2 v 1.18 in Bioconductor v. 3.8
1
gravatar for shepherl
26 days ago by
shepherl ♦♦ 1.3k
United States
shepherl ♦♦ 1.3k wrote:

It is always recommended to use the current versions of package rather than older versions. We can't guarantee that the older version of the package will be able to work without ERROR in the current Bioconductor 3.8 because any one of the dependencies the package relied on will have changed.

RECOMMENDED: If you really want to use DESeq2 it is recommended to use with the latest version of ALL packages. BiocManager::install("DESeq2") and also run BiocManager::valid( ).

NEXT RECOMMENDED If you really need DESeq2 version 1.18, to be safe and consistent to ensure that all your packages are of compatible versions you should install R 3.4 to use Bioc 3.6 where this version occurs.

NOT RECOMMENDED

We cannot guarantee the package will work as expected and as before in Bioc 3.6 because the dependencies of the DESeq2 package will be updated while the package itself is not

You can download the previous tar and install manually by navigating to the landing page for the Bioc 3.6 release. http://bioconductor.org/packages/3.6/bioc/html/DESeq2.html

ADD COMMENTlink modified 26 days ago • written 26 days ago by shepherl ♦♦ 1.3k

Thanks for reply. I will try using a conda environment then.

ADD REPLYlink written 25 days ago by gtechbio0
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