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Old 06-16-2015, 03:14 AM   #1
Location: France

Join Date: Jul 2013
Posts: 20
Default Spearman correlation test: FPKM or counts?

I'm not sure if this is very obvious but I'm not a statistician so I thought I would confirm with the more knowledgeable people on this site.

I would like to do a Spearman correlation between genes on my RNA-Seq data (which I've seen done in various papers). However, they only say "Spearman correlation on gene expression data" and I don't know if that means on counts or FPKM. I've looked around and some papers do FPKM/RPKM (but not necessarily between genes but rather between conditions/treatments) but in message boards, they normally recommend counts but without explaining why. Can anyone enlighten me? Is there any difference between the two?

I've normalized the counts using DESeq size factors.

Thanks for your insight!
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