Hi I am new to R Studio. Recently I tried to use the following commands for instillation of DESeq2 and EdgeR.
library(edgeR)
library(DESeq2)
Unfortunately, both commands are giving an error and aren't executed properly. Can anyone please suggest how to troubleshoot this problem.
I tried to use the command install.packages(DESeq2) or (edgeR). I am getting a warning message.
package âDESeq2â is not available (for R version 3.4.1)
package âedgeRâ is not available (for R version 3.4.1)
Is there anyway to troubleshoot this problem ?
/Aftab
Also I am getting a message, when I try to execute the > library(edgeR) command.
library(edgeR)
Error: package âedgeRâ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
In addition: Warning message:
package âedgeRâ was built under R version 3.5.1
R version 3.5+ has different internals from earlier versions of R (3.4., 3.3., etc). What version of R are you running? You might consider upgrading to >= 3.5.0, since package binaries are now being built for this version of R. You can download the latest version (3.5.1) or older versions from here.
edgeR and DESeq2 are Bioconductor packages, so they canât be installed from CRAN using the usual install.packages() method. Please see their Bioconductor pages for installation instructions:
If you havenât used Bioconductor packages before, itâs also worth making sure you understand how the Bioconductor package, repository and additional packages work, and how things differ from regular R in Bioconductor-land. Start here: https://bioconductor.org/install/
Itâs especially important to make sure that you are running âmatchingâ releases of R and Bioconductor when using Bioconductor packages. Unless you have a very good reason for running an older version of R (and understand how to match that to the appropriate Bioconductor release and package versions), Iâd strongly recommend updating R to the latest version and reinstalling Bioconductor (from the instructions above) before going further.