Hi, I used the script in the following page: http://groups.google.com/group/aroma-affymetrix/web/redundancy-tests to process a dataset of 189 arrays using Human custom refseq CDF version 10, HGU133A_Hs_REFSEQ After I finished fit(plm, verbose=verbose) I got the following message: " Total time for all units across all 189 arrays: 532.37s == 8.87min Total time per unit across all 189 arrays: 0.04s/unit Total time per unit and array: 0.235ms/unit & array Total time for one array (17599 units): 0.07min = 0.00h " When I finished up to the code ces <- getChipEffectSet(plm); theta <- extractMatrix(ces, returnUgcMap=TRUE); theta <- log2(theta); ugcMap <- attr(theta, "unitGroupCellMap"); rownames(theta) <- getUnitNames(getCdf(ces), ugcMap[,"unit"] and type
dim(theta) I found that he total number of probesets is only 11979. "11979 189" If I used affy(rma) and tested on a small number of CEL file from the same dataset, the total number of probesets is 17599. >From the custom cdf document the total number of probeset of this cdf is 17531, so with the "AFFX" probes(68), the total number should be 17599. I was wondering what parameter should be used to get right number of probesets from cdf file for refseq, entrezg, ug respectively Thank you very much. -Yiwen Chen --~--~---------~--~----~------------~-------~--~----~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
