Question: retrieve normalised count data from DESeq2
1
gravatar for Rößti
3.0 years ago by
Rößti20
United Kingdom
Rößti20 wrote:

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 • 5.0k views
ADD COMMENTlink modified 3.0 years ago by andrew.j.skelton735.3k • written 3.0 years ago by Rößti20

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

ADD REPLYlink written 3.0 years ago by Nicolas Rosewick6.8k
4
gravatar for andrew.j.skelton73
3.0 years ago by
London
andrew.j.skelton735.3k wrote:
foo <- counts(object, normalized = TRUE)
write.csv(foo, file="norm_counts.csv") 

Where 'object' is a DESeqDataSet object

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by andrew.j.skelton735.3k

Cheers for that :o)

ADD REPLYlink written 3.0 years ago by Rößti20

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

ADD REPLYlink written 17 months ago by pablo6199140

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.

ADD REPLYlink written 17 months ago by andrew.j.skelton735.3k

Oh, thank you I missed the default parameter.

ADD REPLYlink written 17 months ago by pablo6199140
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