PostFC vs RealFC-which metric to use?

[labra...@gmail.com]

Greetings-

I assist several investigators with RNA-Seq analysis using RSEM-EBSeq.  One question that is often posed is which metric to use to report fold change.  PostFC or RealFC?  Could you offer any advice or direct me to where I might find an answer?

Thanks in advance-

lab rat

[James Chappell]

Hello, 

Did you ever find a good answer for this?

Thanks

[Ning Leng]

Hi,
The posterior fold change estimations will give less extreme values
for low expressers. e.g. if gene1 has mean1 = 5000 and mean2 = 1000,
its FC and PostFC will both be 5. If gene2 has mean1 = 5 and mean2 =
1, its FC will be 5 but its PostFC will be < 5 and closer to 1.
Therefore when we sort the PostFC, gene2 will be less significant than
gene1.
Hope this is helpful.
Ning

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--
Ning Leng, Ph.D
Computational Biologist / Biostatistician
Regenerative Biology Laboratory
Morgridge Institute for Research