Question: Generating RPKM data from dds (DESeq2 pipeline)
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gravatar for harry.horsnell.17
16 months ago by
harry.horsnell.170 wrote:

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 rpkm dds • 275 views
ADD COMMENTlink modified 16 months ago by Michael Love25k • written 16 months ago by harry.horsnell.170
Answer: Generating RPKM data from dds (DESeq2 pipeline)
1
gravatar for Michael Love
16 months ago by
Michael Love25k
United States
Michael Love25k wrote:

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")
ADD COMMENTlink written 16 months ago by Michael Love25k
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