How to get the expression of sample combined the biological replicates in DESeq2?
I have the data of 2 sample, and each sample has 3 replicates RNA-seq.
design = ~ replicate + sample.
i.e.
ddsMatrix <- DESeqDataSetFromMatrix(countData = featureCounts,
colData = sampleTable,
design = ~ replicate + sample)
dds <- DESeq(ddsMatrix)
res <- results(dds)
rld <- rlog(dds)
I found that the rlog or VST function only provided the expression of all replicates of samples. And the results provided the mean log2 expresion of all samples. collapseReplicates was used for technical replicates.
Has any function to export the normalized and log2 transformed expression matrix for each sample?
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rysterzhu •
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Please be more specific. Show which samples you have, how they compare to each other in terms of replication and what the expected output would be (please show output examples, not just text). What is the difference
replicateandsamplein the design formula?