Hello, I have an experiment where I'm comparing a batch A versus B (in biological triplicate: A1/A2/A3/B1/B2/B3). I create the DESeqDataSet, filter by low expression and rRNA, and use VST as a normalization method.

dds <- DESeqDataSetFromMatrix(countData = round(S216_Count_data),                               
                              colData = exp_design,                                        
                              design = ~ Replicate + Treatment)

After that, I'd like to extract the counts from the normalized dds arranged by one of the samples, concretely A1. I tried like this, but I don't think I can select a DESeqDataSet object as if it was a matrix.

norcou <- counts(dds,normalized=TRUE)

head(norcou[order(norcou$A1, decreasing = TRUE), ])

How could I do this? Any help appreciated. Thanks a lot!!

Solution found, I used:

head(norcou[order(norcou[,"A1"], decreasing = TRUE), ], 50)

When you extract the counts from a DESeqDataSet, you get a matrix, not a data.frame, so using counts$A1 won't work. You could use counts[,"A1"] instead.