"Wide" PLS with SVD and multiple categorial predictorsI have a 92,000 columns (genes) x 12 rows (samples) table and would like to use PLS to model treatment effects. However, my treatments (site of origin and temperature) are categorical. If I use discriminant analysis, I can only test one at a time. If I use PLS under the Fit Model platform, I can do a full factorial predictor model, BUT there is no SVD (presumably), so the analysis crashes. Is there something akin to SVD in any PLS-like platform that is NOT discriminant analysis? Alternatively, is it possible to have more than one predictor (X) in the discriminant analysis? I attached the table. Ideally, I would have all 92,960 genes as Y and site of origin, temperature, and their interaction as predictors (3 terms). Maybe my computer is just too old (8 GB RAM with 1.7 Ghz processor)! I am wondering if what I am wanting to do is ONLY achievable with JMP Genomics (which, annoyingly, University of Miami refuses to purchase, even after my nagging!).
AnalyticsRe: "Wide" PLS with SVD and multiple categorial predictorsOne of your options might be one of the penalized regression methods? They don't use SVD, but come at the variable reduction problem from a different analytics point of view...not dimensionality reduction which is baked into PLS. Your computer might still hang because of the number of models that will be 'fit' in the background...but worth a try?
Re: "Wide" PLS with SVD and multiple categorial predictorsGood idea. I am trying it now (1 hr of "hanging" at this point). Even if I reproduce your cancer microarray output, which was ~11,000 columns x 230 rows (Using Partial Least Squares: When Ordinary Least Squares Regression Just Won’t Work ), there is a hang with discriminant analysis, but it's not bad (1-2 minutes), and that study had many more subjects. Maybe if I can weed out those (likely to be majority of) genes with essentially no variation across samples (maybe using response screening or predictor screening), I can retry PLS or Gen-reg with the "informative" genes only since I guess you could argue why would you include a gene with no variation (e.g., a housekeeping gene) in such an analysis?
