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Question: DESerq2 older releases
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gravatar for Eleni Christodoulou
27 days ago by
Singapore
Eleni Christodoulou150 wrote:

Dear Bioc Team,

I have been using DESeq2 for my analysis for the past one year or so. In the meanwhile, I have updated my R and Bioconductor, and I have been using different DESeq2 versions. I would like to go to my old results and see again what were the default options of the DESeq, results and lfcShrink functions back then. When I search, I am only getting the latest version and vignette info. Where can I track the various DESeq2 releases?

Thank you very much.

 

ADD COMMENTlink modified 27 days ago by Michael Love19k • written 27 days ago by Eleni Christodoulou150
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gravatar for Michael Love
27 days ago by
Michael Love19k
United States
Michael Love19k wrote:

Do you want to exactly recreate the old results with the new version of DESeq2?

The best approach to recreate old results table exactly is to instead use the older version of DESeq2. This is possible by downloading the old R and installing Bioconductor again. All versions of DESeq2 are available this way back to version 1.0 released in April 2013.

What old version of Bioc/DESeq2 where you using?

If you want to read about changes, we keep track of those in the NEWS file and in the section of the vignette that talks about changes since the 2014 publication.

ADD COMMENTlink written 27 days ago by Michael Love19k

Thank you very much, Michael.

For the moment, I don't want to recreate the old results, just check what were the default parameters back then. I was using v1.16.1. Thank you for directing me to the NEWS page of DESeq2 Github; It covers my question.

 

ADD REPLYlink written 26 days ago by Eleni Christodoulou150
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