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Use DESeq (1) data with DESeq2 Package?

Hey everyone,

is there a way to deal with data from DESeq packages in current versions of R (e.g. R 4.3.0). I currently deal with this be using a conda environment with old R and DESeq. Then I just run R from the command line, extract the data I need and then go back to RStudio and continue work there. However, it would be great to be able to just load the RData file containing these objects in RStudio and to be able to browse it from there. An example for this would be the data/cds.RData from this publicly available data set

thanks

deseq deseq2
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written by gernophil • gernophil

The DESeq package is deprecated, so whatever setters and getters it and its dependencies used back in the day might be out of date as well in current R. I would really extract all old data into a generic format such as tables that you can save as txt files and load this into the current env. It's imo bad practice to even share data in specific formats such as RData objects as this is, as you see, a problem with versions once deprecation happens. Should always be shared generically, at best independent of package and programming language.

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written by ATpoint ATpoint

I totally agree with you. In all points. It really annoys me every time I need something from this data set.

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written by gernophil • gernophil

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