Dear BioC, I've used the GEOquery package as below to upload GSE7585. This created a list of two ExpressionSets as predicted, one for each platform. > gse<-getGEO("GSE7585",GSEMatrix=TRUE) > names(gse) [1] "GSE7585-GPL3417_series_matrix.txt.gz" "GSE7585-GPL5118_series_matrix.txt.gz" > exprs(gse[[1]])[1:5,] GSM183597 GSM183598 GSM183599 1 1.203 NA NA 2 -1.087 0.874 -1.236 3 0.384 -0.036 0.253 4 -2.443 1.641 NA 5 -1.518 4.661 NA > exprs(gse[[2]])[1:5,] GSM183596 GSM183600 GSM183601 1 -3.237 NA NA 2 -1.500 -1.423 -1.377 3 -0.007 0.144 0.386 4 NA -4.547 NA 5 -0.258 -0.374 -0.492 The experiment consists of three treated groups each performed in duplicate. However, the replicates have been split between two SMD platforms/prints. For example, group A replicate 1 is on GPL3417 and group A replicate 2 is on GPL5118. I would like to combine the two ExpressionSets prior to doing differential expression analysis. The two platforms GPL3417 and GPL5118 correspond to SMD platforms SHGA and SHEU respectively. Looking at each GPL entry, these two arrays appear to have identical features in the same order. Can someone please clarify what is the nature of the difference between the SHGA and SHEU platforms? I'm trying to ascertain if I can "legally" combine the two different ExpressionSets as is. sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] affycoretools_1.14.0 annaffy_1.14.0 KEGG.db_2.2.5 gcrma_2.14.0 matchprobes_1.14.0 biomaRt_1.16.0 GOstats_2.8.0 [8] Category_2.8.0 genefilter_1.22.0 survival_2.34-1 RBGL_1.18.0 annotate_1.20.0 xtable_1.5-4 GO.db_2.2.5 [15] RSQLite_0.7-1 DBI_0.2-4 AnnotationDbi_1.4.0 graph_1.20.0 affy_1.20.0 limma_2.16.2 GEOquery_2.6.0 [22] RCurl_0.91-0 Biobase_2.2.0 loaded via a namespace (and not attached): [1] affyio_1.10.0 cluster_1.11.11 GSEABase_1.4.0 preprocessCore_1.4.0 XML_1.94-0.1 Scott A. Ochsner, Ph.D. NURSA Bioinformatics Molecular and Cellular Biology Baylor College of Medicine Houston, TX. 77030 phone: 713-798-6227