RNA-seq analysis: How to output normalized counts or normalized FPKM values for all genes in each condition from DESeq2 pipeline?

Question

[sclittlerain]

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!

[sclittlerain]

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

Answer 1

[GenoMax]

Normalized counts from DESeq2.
retrieve normalised count data from DESeq2

Answer 2

[Hussain Ather]

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