Question: Calculating RPKM for DESeq
0
gravatar for Whoknows
4.8 years ago by
Whoknows740
Tehran,Iran
Whoknows740 wrote:

Hi friends 

 DESeq works via count table and create DE genes by count fold change, but it's better to know about gene RPKM values.

Is there any possible way to use / show RPKM for DESeq's output? 

And how can i normalized those RPKM values?

tnx.,,

rna-seq deseq tophat htseq • 6.1k views
ADD COMMENTlink modified 4.8 years ago by Devon Ryan90k • written 4.8 years ago by Whoknows740
2

Why is it better to know about RPKM values?  

ADD REPLYlink written 4.8 years ago by Sean Davis25k

 I think  fold-change where generated based on the count table could be a good measurement, but sometimes read count is not practical (for example those  genes with 0 count in one condition) and you have to use another measurement like RPKM and FPKM , Using RPKM make study more robust and confident based on the A.Mortazavi 2008 paper that he said  you can detect with 95% confidence if a transcript has RPKM >11.By the way, using RPKM or FPKM let you to decide for choosing only those genes  with an exact threshold based on your coverage , and other sequencing criterias. 

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by Whoknows740
9
gravatar for Devon Ryan
4.8 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

Do not mix DESeq(2) and RPKMs. RPKMs are inferior to count data for a variety of reasons. Rethink why you want these values to begin with.

If you want to convert count data to RPKMs, take the normalized counts produced by DESeq2 (or edgeR, or any similar tool), divide them by the gene length in KB (typically one would just sum the exons) and divide by 1 million.

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Devon Ryan90k

Hi, 

I want to use rpkm() function in edgeR to do this but i am facing problems with gene length do you know what am I might be doing wrong?

 

ADD REPLYlink written 3.6 years ago by kanika.15160
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