[BioC] (no subject)

[Fangxin Hong]

> The Questions:
> 1) Is this an ok model to use, or is it better to include the intercept?
doesn't matter whether you include intercept or not, they are equivalent
models


> 2) How would I report either linear model via an equation?
gene expression at time t under condition i=true gene expression at time t
under condition i + noise


> 3) Should one perform a multiple testing correction on the FStat p-values?
If yo want to control overall significance of your identification, you
should.

> 4) Should the genes supplied by the signficant FStats(fit3) have all
> non-zero
> values in the 6 contrasts? (they do not)
I am not sure about this, but I think the FState still test each value
separately. You can select genes who have non-zero values in the 6
contrasts manually.


> 5) If I would like to look at all genes that are differentially expressed
> between time points 2 and 3 across genotypes, is it best to simply
> extract these from the significant FStats group that have nonzero values
> in contrasts 1 and 2, or choose the intersection between G1 and G2?
It depends on your data and what you want. G1 and G2 give you top 1000
genes no matter they are significant or not. Fstats give you all
significant genes which maybe less or more than 1000.
Maybe you can start with Fstat result as it has significnat genes.


Fangxin

-- 
Fangxin Hong, Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu