Question: Professor of Biology
0
gravatar for bslocum
2.9 years ago by
bslocum0
bslocum0 wrote:

I have just learned how to use DESeq2 and had written a tutorial for my bioinformatics class.  Unfortunately, I made the mistake of updating R to version 3.3.2 (running Mac OS X 10.11) and it seems that DESeq2 is no longer supported.  This is hugely disappointing.  It ran on R-3.3.0 (may 2016), but I’m having trouble getting this archived version back from CRAN.

Any suggestions would be appreciated.

Here's the error message from R console:

 

install.packages("DESeq2")
Warning in install.packages :
  package ‘DESeq2’ is not available (for R version 3.3.2)

deseq2 • 367 views
ADD COMMENTlink modified 2.9 years ago by Martin Morgan ♦♦ 23k • written 2.9 years ago by bslocum0
Answer: Professor of Biology
2
gravatar for Peter Langfelder
2.9 years ago by
United States
Peter Langfelder2.2k wrote:

The mistake is using install.packages() rather than biocLite() to do the installation. From the DESeq2 Bioconductor page:

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")

 

ADD COMMENTlink written 2.9 years ago by Peter Langfelder2.2k
Answer: Professor of Biology
1
gravatar for Martin Morgan
2.9 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

Please try to install the package following the Bioconductor installation instructions preset on every package landing page

source("https://bioconductor.org/biocLIite.R")
biocLite("DESeq2")

The package is very much available and actively supported.

Be sure to validate your current installation, since if you have been using install.packages() directly it is likely to be invalid

BiocInstaller::biocValid()
ADD COMMENTlink written 2.9 years ago by Martin Morgan ♦♦ 23k
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