I'm wondering if anybody could help me. Iìm dealing with REST 2009 and its output:
It says: "Gene1 is down-regulated in sample group (in comparison to control group) by a mean factor of 0.454 (S.E. range is 0.312-0.680). Gene1 sample group is different to control group. P(H1)=0.003"
Now, what I can't understand is:
- is the 0.454 factor a fold change?
- how can I plot the Standard error? shouldn't it be the error range around the mean (so that it's the value on both sides?)
The other thing that is not clear to me is:
- REST tells you which genes are significantly up and down regulated, but what about the others? What about the genes whose expression value is 0.519 (for example) that are not indicated as up/down regulated though? Should I think that since the expression value is <1 they are down regulated but not significantly "enough"?
I've been reading here and there but can't find any idea.
I hope some of you can shed some light.
understanding REST2009 output
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