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

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