Question: Find the expected counts in DESeq2 output
0
gravatar for cwliu2014
9 weeks ago by
cwliu20140
cwliu20140 wrote:

Hello,

I'm processing RNA-seq data (sampleA, sampleB) with featureCounts, and DE analysis with DESeq2. In the DESeq2 output, there are only baseMean, log2FoldChange...

I would like to extract the expected counts calculated by DESeq2 (already normalized, not the raw read counts from featureCounts).

Is there anyone knowing how to extract the expected counts value for each sample?

For example, geneID sampleA sampleB GeneA 5.666 4.333 GeneB 4.444 3.222 GeneC 4.111 7.555 . . .

Thanks in advance.

Edward

deseq2 • 111 views
ADD COMMENTlink modified 9 weeks ago by swbarnes2170 • written 9 weeks ago by cwliu20140
Answer: Find the expected counts in DESeq2 output
0
gravatar for Michael Love
9 weeks ago by
Michael Love23k
United States
Michael Love23k wrote:

DESeq2 operates on raw counts. It doesn’t use normalized counts internally. You can generate counts / size factors, see the vignette and ?counts

ADD COMMENTlink written 9 weeks ago by Michael Love23k
Answer: Find the expected counts in DESeq2 output
0
gravatar for swbarnes2
9 weeks ago by
swbarnes2170
swbarnes2170 wrote:
counts(dds, normalized = TRUE)
ADD COMMENTlink written 9 weeks ago by swbarnes2170
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