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Old 11-03-2010, 11:15 AM   #1
rnaseq
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Default fold change for genes with 0 reads

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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Old 11-04-2010, 07:27 PM   #2
malachig
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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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Old 11-04-2010, 07:44 PM   #3
ECO
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Closed. Thanks malachig.
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