This is a test version of Biostars. For the public version, visit https://www.biostars.org.
retrieve normalised count data from DESeq2

Hello, sorry if this is a really stupid question but I have been struggling with this for a week or so now.

Basically I carried out a bacterial RNA-seq on 2 conditions in triplicates. After doing some analysis using DESeq2 it is looking like there is no differential expression between the 2 conditions however, is there a way that I can save the normalised count data to a cvs file so that I can check the quality of the replicates?

Thanks

rna-seq
• 15,977 views • link
updated by Ram Ram • written by Rößti • Rößti

FYI you can do a PCAplot to check wheter your replicates cluster together .. or not. Check DESeq2 vignette for PCAplot

• 0 views • link
written by Nicolas Rosewick Nicolas Rosewick

1 answer 

foo <- counts(object, normalized = TRUE)
write.csv(foo, file="norm_counts.csv")

where object is a DESeqDataSet object

• 0 views • link
updated by Ram Ram • written by andrew.j.skelton73 andrew.j.skelton73

And to obtain the count matrix before the normalization just change normalized = TRUE for normalized = FALSE?

• 0 views • link
written by pablo61991 • pablo61991

Yes, or don't include the normalized parameter as when you look at the function's help page (?DESeq2::counts), you'll see that it's FALSE by default.

• 0 views • link
written by andrew.j.skelton73 andrew.j.skelton73

Oh, thank you I missed the default parameter.

• 0 views • link
written by pablo61991 • pablo61991

Thank you, andrew, your script worked out!

But when I extract the DESeqDataSet object (dds), normalized counts table don't have Gene Ids, only numbers, like that:

gene id         BSR111-Med-46                   BSR112-Med-58
1               2.87573335679571                2.58809911711063
2               31.6330669247528                51.7619823422126

How can I get the normalized count data with gene ids?

Thank you again

• 1 views • link
updated by Ram Ram • written by LuisNagano • LuisNagano

Check the rownames on your input matrix. If they're not set, then they'll default from 1:n

• 0 views • link
written by andrew.j.skelton73 andrew.j.skelton73

Log in to answer this question.

More posts like this