Generating RPKM data from dds (DESeq2 pipeline)
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@harryhorsnell17-15582
Last seen 6.5 years ago

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

deseq2 dds RPKM • 1.2k views
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@mikelove
Last seen 1 hour ago
United States

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")
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