Dear all,

I have just generated my  DESeqDataSet and I am curious about how I can generate RPKM data from this

dds <- DESeqDataSet(se, design = ~ Cell + Hour )

I am quite new to the DESeq2 workflow so any suggestions will be much appreciated 

Many thanks,

Harry Horsnell

We have an fpkm() function, try this code below to pop up all the functions. But we can't generate this with just a count matrix. You need to provide the gene lengths. The best way to get abundance is to use a transcript quantifier like Salmon, then import with tximport. The abundances will be available as txi$abundance.

> help(package="DESeq2",help_type="html")