Hello all, I know the general question of "should I summarize/average/etc probes that map to the same gene?" has been discussed many times before. But, I feel that it might be slightly different on the Illumina platform (at least for the Mouse chip, which is the one I have been using). For non-control probes, there simply is no advantage to using probe summarized data relative to target summarized data, since you basically have the same number of distinct sequences. So, even though the probe names have changed, and there appear to be ~70k of them, there are only ~46k different probe sequences, which just about map nicely to the number of targets... The numbers: > length(as.list(lumiMouseV1TARGETID2NUID)) [1] 46116 > length(as.list(lumiMouseV1PROBEID2NUID)) [1] 70182 > length(unique(as.list(lumiMouseV1PROBEID2NUID))) [1] 46120 Cheers, Cei sessionInfo() R version 2.7.0 (2008-04-22) i386-apple-darwin8.10.1 locale: C attached base packages: [1] stats graphics grDevices datasets tools utils methods [8] base other attached packages: [1] lumiMouseV1_1.3.1 lumiMouseAll.db_1.2.0 AnnotationDbi_1.2.0 [4] RSQLite_0.6-8 DBI_0.2-4 lumi_1.6.0 [7] mgcv_1.3-30 affy_1.18.0 preprocessCore_1.2.0 [10] affyio_1.8.0 Biobase_2.0.0 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.