Question: rna seq - deseq2
0
gravatar for dimitrischat
2.3 years ago by
dimitrischat110
dimitrischat110 wrote:

Hello all again, i was using cuffdiff (the last step) thus far to do rna-seq analysis but as i ve read and been told cuffdiff is outdated and now i have been using deseq2 ( i got no idea of R but with the help of this link : https://dwheelerau.com/2014/02/17/how-to-use-deseq2-to-analyse-rnaseq-data/ i was able to achieve something ). Results from cuffdiff also had basemeanA basemeanB ( two conditions or two samples ) but deseq2 just gives 1. Can someone tell me the code in R to add so i can get the basemean for each sample/condition ?

rna-seq • 656 views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 2.3 years ago by dimitrischat110
2

Is there a reason you want that? You already have the overall base mean, having that per-group isn't then informative.

ADD REPLYlink written 2.3 years ago by Devon Ryan94k
1

To get it in R, you don't have to do much more than mean(x) where x is the vector containing the column that you want to get the average of.

However, I side with @DevonRyan. Why would you want that?

ADD REPLYlink written 2.3 years ago by Macspider3.0k
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