using DESeq2 v 1.18 in Bioconductor v. 3.8
1
0
Entering edit mode
gtechbio ▴ 10
@gtechbio-13996
Last seen 10 months ago
Spain

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 • 787 views
ADD COMMENT
1
Entering edit mode
shepherl 3.8k
@lshep
Last seen 1 hour ago
United States

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 COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 767 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6