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Question: retrieve normalised count data from DESeq2
2
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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

ADD COMMENTlink 4.4 years ago Rößti • 30 • updated 4.4 years ago andrew.j.skelton73 5.7k
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FYI you can do a PCAplot to check wheter your replicates cluster together .. or not. Check DESeq2 vignette for PCAplot

ADD REPLYlink 4.4 years ago
Nicolas Rosewick
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foo <- counts(object, normalized = TRUE)
write.csv(foo, file="norm_counts.csv") 

Where 'object' is a DESeqDataSet object

ADD COMMENTlink 4.4 years ago andrew.j.skelton73 5.7k
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Cheers for that :o)

ADD REPLYlink 4.4 years ago
Rößti
• 30
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And to obtain the count matrix before the normalization just change normalized = TRUE for normalized = FALSE?

ADD REPLYlink 2.8 years ago
pablo61991
• 70
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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 2.8 years ago
andrew.j.skelton73
5.7k
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Oh, thank you I missed the default parameter.

ADD REPLYlink 2.8 years ago
pablo61991
• 70
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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 15 months ago
LuisNagano
• 10
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Check the rownames on your input matrix. If they're not set, then they'll default from 1:n

ADD REPLYlink 12 months ago
andrew.j.skelton73
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