handle zero in raw read count

[BFM]

Hi

i have applied DESeq to my raw read counts from htseq. I have removed genes which haveall raw read counts as zero.

But DESeq is unabel to handle the remaining zeros. For example i am comparing the expression and raw raeds are 0 and 200. But instead of giving me any logfold change value it is showing infinity.

What whould be a good way to handle these zeros and i want to add that factor to all non zero values as well (just to be consistant)

[blakeoft]

I suppose you could change the zeros into ones. As far as I know, it's pretty common to plot log(x + 1) instead of log(x) to avoid this infinity issue.

[dpryan]

Infinity is the correct fold-change. There's no reason to change any of those zeros.