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Question: IHW Package for R 3.2.5
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gravatar for bekah
7 months ago by
bekah0
bekah0 wrote:

Hiya, I'm trying to find a version of IHW that is compatible with R 3.2.5 in which I am running DESeq2, but haven't had any luck - is there an alternative package that does a similar function that I could use instead that you would recommend please?

Best wishes

Rebekah

ADD COMMENTlink modified 7 months ago • written 7 months ago by bekah0

Cheers- I'll see what versions are available,!

ADD REPLYlink written 7 months ago by bekah0

Mike's suggestion is the most elegant one and I'd recommend you go that route. If you really can't move to another version, you could probably manually download IHW and its dependencies and manually change the R version requirements in the `DESCRIPTION` file. It should probably work (although not tested).

ADD REPLYlink written 7 months ago by Nikos Ignatiadis110

cheers - is all sorted, managed to call the latest R version and run as admin to get the packages needed to install 

ADD REPLYlink written 7 months ago by bekah0
1
gravatar for Michael Love
7 months ago by
Michael Love14k
United States
Michael Love14k wrote:

IHW was released for R 3.3 (this is on the package landing page under "In Bioconductor since...")

Short answer: you could just use the default independent filtering if you can't get access to a more recent version of R. This happens within results() without you needing to specify anything.

Longer answer: If it's because you're on a cluster, and they only provide older versions of R, I'm of the opinion that whoever administers the cluster should help to keep R up-to-date, so users can access the latest software. I build R from source on my cluster for developing packages and it usually takes me about a day to get everything I need to build successfully, but if I can do it, I'm sure a cluster administrator can do it. It should be possible for the cluster administrators to make multiple versions of R available, such that users can reproduce Bioconductor analyses using packages tied to older R versions, while still making the current versions available.

When I type module load r/<tab> on my cluster I see:

r/2.15.1  r/3.0.1   r/3.1.1   r/3.2.2   r/3.3.1

 

ADD COMMENTlink modified 7 months ago • written 7 months ago by Michael Love14k
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