Question: How to get the expression of sample combined the biological replicates in DESeq2?
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gravatar for rysterzhu
9 weeks ago by
rysterzhu0
rysterzhu0 wrote:

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?

rna-seq deseq2 • 121 views
ADD COMMENTlink modified 8 weeks ago • written 9 weeks ago by rysterzhu0

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 replicate and sample in the design formula?

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by ATpoint28k
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