[BioC] edgeR

[puvan001 at umn.edu]

I am new to edgeR and I am not a statistician. I analyzed my RNA seq data,
I got the results as 200 up regulated and 97 down regulated genes. My
questions are-
1. What is the cut off value used by edgeR to say upregulated versus down
regulated? I am little bit confused here. When I checked the log fold
changes I couldn't come to a conclusion. When I counted the number of genes
<0, the number is more than 97. Am I doing some thing wrong?

2. If I want to do some pathway analysis, I am wondering which value I have
to use. When I use log fold change values, some genes are not identified as
differentially expressed though I gave different cut off values.

Can somebody help me?



Sumathy