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

[Anand C. Patel]

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.

The pData of the exprSet I have runs as follows:
> pData(eset)
                               Day Strain Condition
whatever 1.CEL                   0      1         0

Day is 0, 3, 8, or 21
Strain is 1, 2, or 3
Condition is 0, 1, or 2

How do I get Bioconductor to look at the covariates independently and
together, and how do I get it to look at the subsets?

Data is in triplicate per overall experimental condition (combination of day,
strain, and condition), so there are a total of 63 arrays.
(d0 doesn't have Condition 1 or 2, just 0 as they're naive control animals)

Help!

Thanks,
Anand C. Patel, MD
Fellow, Pediatric Pulmonology
Washington University St. Louis