Question: retrieve normalised count data from DESeq2
2
gravatar for Rößti
3.2 years ago by
Rößti30
United Kingdom
Rößti30 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 • 5.4k views
ADD COMMENTlink modified 3.2 years ago by andrew.j.skelton735.5k • written 3.2 years ago by Rößti30

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

ADD REPLYlink written 3.2 years ago by Nicolas Rosewick7.2k
4
gravatar for andrew.j.skelton73
3.2 years ago by
London
andrew.j.skelton735.5k wrote:
foo <- counts(object, normalized = TRUE)
write.csv(foo, file="norm_counts.csv") 

Where 'object' is a DESeqDataSet object

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by andrew.j.skelton735.5k

Cheers for that :o)

ADD REPLYlink written 3.2 years ago by Rößti30

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

ADD REPLYlink written 20 months ago by pablo6199170

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 20 months ago by andrew.j.skelton735.5k

Oh, thank you I missed the default parameter.

ADD REPLYlink written 20 months ago by pablo6199170

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

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by LuisNagano10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1148 users visited in the last hour