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Question: Get normalized COUNTS Deseq2
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gravatar for anaQ
12 days ago by
anaQ0
anaQ0 wrote:

Hi, i'm trying to get the normalized counts only, for all the replicates and genes of my data (named "14vs48)". 

I'm trying this command:

table_counts <- counts(results14vs48, normalized=TRUE)

but i get this error message:

unable to find an inherited method for function ‘counts’ for signature ‘"DESeqResults"’

I havent found a similar question on the internet. Why is this happening?

ADD COMMENTlink modified 12 days ago by Steve Lianoglou12k • written 12 days ago by anaQ0
0
gravatar for Steve Lianoglou
12 days ago by
Denali
Steve Lianoglou12k wrote:

You need to call counts() on your DESeqDataSet object. This is the object that stores your count data.

You are currently calling counts() and the object you received from calling results(...) on your DESeqDataSet object. This results object merely holdes the statistics for a particular contrast of interest from your dataset.

ADD COMMENTlink written 12 days ago by Steve Lianoglou12k

thank you so much!

ADD REPLYlink written 11 days ago by anaQ0
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