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Old 11-03-2010, 03:01 AM   #4
nkwuji
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Location: Dublin

Join Date: Mar 2010
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Thx RockChalkJayhawk.

I will think about this part, though the result seems to be a little weird on genes expressed at low levels. For example, for this gene expressed in one sample with FPKM of 8, and in the other sample with FPKM of 0, the result is shown as NOTEST. But for the other gene, in one sample, the FPKM is 0.25, and in the other sample is 0. THe result is OK, and significant.

Possibly it can be explained by the second gene is longer, and the min-alignment-count could be higher than default setting and got the test significant. But I think it may be better to limit the result by FPKM (or average coverage) other than total fragments(or reads), otherwise, it may have bias on longer genes.
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