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Question: Does edgeR accept decimal / integer read counts for differential expression ?
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gravatar for Padhmanand.Sudhakar
5 months ago by
Padhmanand.Sudhakar0 wrote:

Hi 

I have read counts (based on multiple mapping) for small RNAs. Since it is normalized for multiple mapping, some of the read counts have decimalized values on which I would like to perform differential expression (condition A vs B). 

 

My specific question is if edgeR accept decimal / integer read counts for differential expression ?

 

Best regards

Paddy

ADD COMMENTlink modified 5 months ago by Gordon Smyth32k • written 5 months ago by Padhmanand.Sudhakar0
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gravatar for Gordon Smyth
5 months ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:

Yes it does. All the edgeR analysis pipelines accept fractional counts. edgeR uses a continuous version of the negative binomial distribution so that it can work directly with fractional counts without rounding them to integers.

ADD COMMENTlink modified 5 months ago • written 5 months ago by Gordon Smyth32k
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