I would like to know if there are any recommendations on re-running 'aroma' on a subset of samples. In my case, the first pass through a dataset (Affy Mouse expression) revealed an outlier array. I would now like to re-run with the outlier array removed.
1) Is extract() the recommended way to do sample subsetting: cs <- extract(cs, 2:length(cs)) ## first array is the outlier Using brackets [] produced a list, so I presume that does not work. 2) An aroma re-run quickly returns at this point, because the output files already exist. It appears necessary to remove the output files first. The following code appears apropos (pulled from http://www.agron-omics.eu/uploads/Tiling%20array%20files/agronomicsTools01.r): >>> CODE force <- TRUE bc <- RmaBackgroundCorrection(celSet); if (force & !is.null(getOutputFiles(bc))){ file.remove(getOutputFiles(bc)) } csBC <- process(bc, verbose=verbose, force=force, overwrite=force); qn <- QuantileNormalization(csBC, typesToUpdate="pm"); if (force) file.remove(getTargetDistributionPathname(qn)) clearCache(qn) if (force & !is.null(getOutputFiles(qn))){ file.remove(getOutputFiles(qn)) } csN <- process(qn, verbose=verbose, force=force); plm <- RmaPlm(csN); fit(plm, unit=NULL, verbose=verbose, force=force) <<< END OF CODE I feel having the output files consistent (i.e. not mixed from different runs) is a good idea. The flip side is, analyzing subsets of samples in parallel (e.g. before a strict decision on outliers has been made) is probably best handled by treating each one as a separate dataset, starting from the original CEL files. Regards, _Taku -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
