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Old 04-15-2011, 03:24 AM   #2
dahlo
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Location: Uppsala University, Sweden

Join Date: Sep 2010
Posts: 8
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Hello

Regarding the huge ratios, i think they are hard to avoid. There is no other way to handle the scenarios where you have a gene that is switched on/off, that i know of.

If you were to plot your ratio values, you would likely see most of them around 0 - a couple of thousand perhaps, and some scattered outliers with ridiculous high values. You can then set a suitable cutoff and say that all genes with a ratio higher than X (say 1e10 or 1e20) are genes that have been turned off or on. It is pointless to sort them with respect to their ratio size, since they all should have Inf.

Computers don't like to divide by 0, so a small number (like 1e-500 or so) has been added to the FPKMy in the division to keep the program from crashing, since many programming languages can't handle infinite numbers.

Cheers
Dahlo
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