fold change for genes with 0 reads

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rnaseq

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Join Date: Dec 2009

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#1

fold change for genes with 0 reads

11-03-2010, 11:15 AM

I am comparing Illumina RNA-seq data sets for differentially expressed genes. A significant number of genes have 0 reads in one of the two conditions. What is the best way to include these genes? Is it acceptable to subsitute the 0 in the numerator or denominator with another number to get an approximate idea of the fold change?

Thanks!
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malachig

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#2

11-04-2010, 07:27 PM

This appears to be a cross post. FAQ says not to do this...

In case anyone lands on this one, the post that has generated discussion is here.
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ECO

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#3

11-04-2010, 07:44 PM

Closed. Thanks malachig.
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