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Old 05-08-2015, 09:07 AM   #1
Robby
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Location: Germany

Join Date: Mar 2011
Posts: 68
Default DESeq2 version problems

Hello,

How can I receive the newest version of DESeq2 for Ubuntu? I have the following problem:

I had to change my computer. On both computer R version 3.02 is installed on a Linux system. On both computer I used the following command to install DESeq2:

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

On my old computer I installed DESeq already a couple of months ago, but there it is version 1.4.5, while on my new computer the version is 1.2.10.

Has anyone an idea, how I can receive the newer version also on my new computer? On the DESeq2-Homepage they even mention that version 1.8.1 is released.

Hope you can help
Best
Robby
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Old 05-09-2015, 06:11 AM   #2
Michael Love
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Default

Bioconductor (and all packages which biocLite() installs for you) is linked to your R version. The point of Bioconductor is to ensure that all the packages will work together, and will work with the version of R you have. You need to install the latest version of R (3.2.0) to get Bioconductor version 3.1 which contains DESeq2 version 1.8

see:

http://bioconductor.org/install
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Old 05-10-2015, 02:01 AM   #3
Robby
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Location: Germany

Join Date: Mar 2011
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OK thanks. I used the the following command to install R:
sudo apt-get install r-base
I thought that will install the newest R version. But this was not the case. Now I managed to install the correct R and Bioconductor version and everything works . Thanks for your help!
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