Question: Find the expected counts in DESeq2 output
0
gravatar for cwliu2014
7 days 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 • 73 views
ADD COMMENTlink modified 7 days ago by swbarnes290 • written 7 days ago by cwliu20140
Answer: Find the expected counts in DESeq2 output
0
gravatar for Michael Love
7 days ago by
Michael Love22k
United States
Michael Love22k 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 7 days ago by Michael Love22k
Answer: Find the expected counts in DESeq2 output
0
gravatar for swbarnes2
7 days ago by
swbarnes290
swbarnes290 wrote:
counts(dds, normalized = TRUE)
ADD COMMENTlink written 7 days ago by swbarnes290
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