[BioC] methodological question

[Phguardiol at aol.com]

Hi,

Here is my question and I hope it fits into the BioC support group (!): 
I have one cell line A with a deficient gene and another one B with the 
corrected gene (same cell line indeed with gene transfered). 
I have some Xpts conducted under normal cell culture conditions and some 
others in which I have added a stressing agent - some at 10 nM and some 
others at 100 nM ie 2 different concentrations -. 
Let say the question is what are the genes that are differentially expressed 
between A and B ? 
I was planning to do a first comparison A vs B under normal cell culture 
conditions, then a second for those ran at 10 nM of the stressing agent, then 
a third one at the 100 nM dose... 
But I was wondering if another one, pooling all the A chips versus all the B 
chips -whatever the stressing agent is added or not and using the average 
signal- should give me more power to detect some kind of differences because 
of the increase number of chips in this case ? Said differently I guess it 
might possible there to pick genes that have not been identified in any 
previous comparisons just because of the lack of power / not enough chips ?
Then in this comparison could I say that I was looking for genes that are 
differentially expressed between A and B whatever the conditions were, ie 
with or without drug, means genes that are or seem to be invariantly 
dysregulated in cells A ? 
The other approach I see is to do all the first comparisons for each subgroup 
and to do Venn Diagram Union: under normal cell culture conditions U drug 10 
nM U drug 100 nM but then I am not taking the maximum power of the system 
since I reduce the number of chips per comparison ? 
It seems that another approach is proposed in T Speed book ie factorial 
design Xpts but I m waiting for the book  ?!
thanks for any help / advise 
Philippe

	[[alternate HTML version deleted]]