Question: RNA-seq analysis: How to output normalized counts or normalized FPKM values for all genes in each condition from DESeq2 pipeline?
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gravatar for sclittlerain
5 days ago by
sclittlerain0 wrote:

I am using a “star-featurecounts-DESeq2” pipeline to perform transcriptome comparison between several conditions (more than 2 conditions) of my samples. I noticed that my final differential expression lists contains only 7 columns: gene ID, baseMean,log2FoldChange,lfcSE,stat,pvalue and padj. I didn’t find any column that contained normalized counts or normalized FPKM values. I need these normalized counts or normalized FPKM values to generate a master gene expression matrix to do co-expression among all conditions later on. Could anyone guide me on the right way to have DEseq2 generate the output with additional column that contains normalized counts or normalized FPKM values for each genes in the final differential expression list? Thanks!

rna-seq • 106 views
ADD COMMENTlink modified 5 days ago • written 5 days ago by sclittlerain0

Normalized counts from DESeq2.
retrieve normalised count data from DESeq2

ADD REPLYlink modified 5 days ago • written 5 days ago by genomax39k

Thanks, Hussain. I figure it out how to output the the normailzed counts using your suggestion.

ADD REPLYlink modified 5 days ago • written 5 days ago by sclittlerain0
0
gravatar for Hussain Ather
5 days ago by
Hussain Ather510
National Institutes of Health, Bethesda, MD
Hussain Ather510 wrote:

Use counts(dds, normalized=TRUE) to generate normalized counts.

ADD COMMENTlink written 5 days ago by Hussain Ather510
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