Dear edgeR users and developersï¼
I have few questions about edgeR when recently I use it for 454
pyrosequencing data:
1. prior.n
According to users' manual, we may not use too low prior.n in
moderated tagwise dispersion approach. But in my dataset, there are
more than 15 samples in each comparison group and the freedom is
larger than 30. prior.n <- estimateSmoothing(d) gives 0.0005329. So I
am wondering if I could use 0.0005329 since I have rather big number
of samples in each group. Or I should adjust prior.n into 10 according
to the manual's suggestion.
2. TMM
I am not sure if this is also applicable to 454 microbiota data.
I suppose I should do TMM normalization as well since the
normalization factors from my samples have a big variation (f is from
0.41 to 4.58). Is that right?
3. p_value
According to your experience, is it reasonable and reliable to
use p_value < 0.05 as significance criteria? or only <0.01 can be
reliable.
I am a new users in this package and hope you may give some
suggestions. Many thanks!
Ying Ye
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