Question: RNA-seq analysis: How to output normalized counts or normalized FPKM values for all genes in each condition from DESeq2 pipeline?
0
gravatar for sclittlerain
20 months 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 • 1.7k views
ADD COMMENTlink modified 20 months ago • written 20 months ago by sclittlerain0

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

ADD REPLYlink modified 20 months ago • written 20 months ago by sclittlerain0
1
gravatar for genomax
20 months ago by
genomax70k
United States
genomax70k wrote:

Normalized counts from DESeq2.
retrieve normalised count data from DESeq2

ADD COMMENTlink modified 20 months ago • written 20 months ago by genomax70k
1
gravatar for Hussain Ather
20 months ago by
Hussain Ather940
National Institutes of Health, Bethesda, MD
Hussain Ather940 wrote:

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

ADD COMMENTlink written 20 months ago by Hussain Ather940
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