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Old 05-19-2011, 06:47 AM   #1
Puva
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I used edgeR to find differntially expressed genes of my RNA-seq data. I am little bit confused with one observation. A couple of genes are only turned on in my treatment group (ie 0 reads in my control group). But I got a particular value (for example 30) of fold change. What my confusion is, if there is no expression at all in my control group, how can edgeR give this value? Can anybody help me?
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Old 05-19-2011, 08:31 AM   #2
dariober
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Quote:
Originally Posted by Puva View Post
I used edgeR to find differntially expressed genes of my RNA-seq data. I am little bit confused with one observation. A couple of genes are only turned on in my treatment group (ie 0 reads in my control group). But I got a particular value (for example 30) of fold change. What my confusion is, if there is no expression at all in my control group, how can edgeR give this value? Can anybody help me?
The log fold change of a count vs 0 is infinity (or -infinity). So edgeR adds a small quantity to 0 in order to get some fold change very large (30 or so as you can see) but not infinite.

Hope this helps...

Dario
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Old 05-19-2011, 09:04 AM   #3
Puva
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Thanks! It makes sense.
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