Originally posted by vebaev
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If you have 0 counts in one condition and hundreds of counts in other, this is most likely a valid signal, and DESeq should indicate this with a small p value. Of course, the fold change estimate is not to useful but that is a general problem if one of conditions has very low counts -
Yes Simon,
the =Inf are coming from rows where one of the groups are 0 and other is some reads (sometimes 5 simetimes 500)
I also found your post in other topic about these =Inf that if the last 2 columns the values are too big or close to zero I should discard these rows from further analysis?Last edited by vebaev; 08-19-2011, 12:43 AM.------------
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