[BioC] General statistical question 2 colour data

[Anja Schiel]

Dear all,

I have some basic statistical questions and which packages might provide
tools to answer those.

I am running R 2.0.1 + Bioconductor under Debian testing.

I did have a look at the archives but did not find any satisfying
answers (or I didn't search the right way) and since I have only a
limited statistical background I need some pointers/help.

1.
I have 4 sets of mice (wt vs treated) that have been hybridized as
random pairs to a total of 8 oligo arrays (each pair twice as a dye swap
pair). Each array is spotted in duplo.

I would like to not only identify genes that are differentially
expressed between the two experimental groups (wt and treated) but I
also want to extract the effect of the treatment from the mouse
individual effect of each mouse-pair(this effect could then be used as a
factor in determining the required number of animals for a new
experiment). I assume that each hybridisation will differ from the other
pairs due to the mouse-(or patient-)effect. Is there an easy way to
extract this information?

Any hint to which package I should use or vignettes that discuss this
issue would be greatly appreciated (if I know where to look for I
usually get things running).

2.
I do not have only on treatment but actually two treatments. The groups
were hybridised in a loop design. I was told that I could only perform
an ANOVA if I split the ratios (is this true?). I was also told this was
dangerous business if I could not guarantee that the correlation between
the individual green and red channels of each experimental group was
"good" enough.

My question is therefore, how can I check the correlation?
Should I run a normalisation on the individual channels of each array or
do I have to test the correlation on raw channel data (which differ quit
a lot, hence the normalization, at least thats what I thought).
What is a good correlation anyhow? Our Oligo-arrays are printed on home
made slides, so quality is always an issue, where do I have to draw a
line?

And, if I have to work with ratios after all is there no other
statistical approach to the loop design?

I fear that these are very basic questions you probably get every now
and then but I would greatly appreciate any help.

Thanks, Anja






-- 
Anja E. Schiel, Ph.D.
Departments of General Internal Medicine and Human Genetics
Leiden University Medical Center
PO Box 9503
2300 RA Leiden
The Netherlands 
tel: -31-(0)71-5276067
fax: -31-(0)71-5276075