[BioC] analysis post gcrma (factdesign? multtest? siggenes?)

[James W. MacDonald]

Anand C. Patel wrote:
> After much reading, careful work, and success in managing to:
> 1.  load my arrays (moe430a) into bioC
> 2.  get justgcrma to normalize them (windows -- memory limits with gcrma)
> 3.  successfully add pData to them
> 
> I am now sitting with a set of normalized data.  I think (think) I should use
> factDesign or multtest to assess the impact of the various covariates, but at
> this point get VERY confused by the vignettes.

If you are getting confused by the vignettes, then you are likely 
fighting two battles at once (understanding the functions and 
understanding the statistics).

I doubt an email correspondence will be enough to alleviate your 
confusion, and would highly recommend consulting with a local 
statistician. Maybe there is someone in the Siteman Cancer Center 
Bioinformatics Core who could help you?

Best,

Jim


-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109