Question: Find the expected counts in DESeq2 output
0
gravatar for cwliu2014
4 months 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 • 138 views
ADD COMMENTlink modified 4 months ago by swbarnes2210 • written 4 months ago by cwliu20140
Answer: Find the expected counts in DESeq2 output
0
gravatar for Michael Love
4 months ago by
Michael Love24k
United States
Michael Love24k 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 4 months ago by Michael Love24k
Answer: Find the expected counts in DESeq2 output
0
gravatar for swbarnes2
4 months ago by
swbarnes2210
swbarnes2210 wrote:
counts(dds, normalized = TRUE)
ADD COMMENTlink written 4 months ago by swbarnes2210
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 295 users visited in the last hour