Already in reference to the post in biocondcutor mailing list (https:/ /stat.ethz.ch/pipermail/bioconductor/2012-February/043741.html) , Iam facing the same issues: universe<-mget(c("244901_at", "244902_at", "244903_at", "244904_at", "244905_at", + "244906_at", "244907_at", "244908_at", "244909_at", "244910_s_at", + "244911_at", "244912_at", "244913_at", "244914_at", "244915_s_at", + "244916_at", "244917_at", "244918_at", "244919_at", "244920_s_at", + "244921_s_at", "244922_s_at", "244923_s_at", "244924_at", "244925_at", + "244926_s_at", "244927_at", "244928_s_at", "244929_at", "244930_at", + "244931_at", "244932_at", "244933_at", "244934_at", "244935_at", + "244936_at", "244937_at", "244938_at", "244939_at", "244940_at", + "244941_at", "244942_at", "244943_at", "244944_s_at", "244945_at", + "244946_at", "244947_at", "244948_at", "244949_at", "244950_at", + "244951_s_at", "244952_at", "244953_s_at", "244954_s_at", "244955_at", + "244956_s_at", "244957_at", "244958_at", "244959_s_at", "244960_at", + "244961_at", "244962_at", "244963_at", "244964_at", "244965_at", + "244966_at", "244967_at", "244968_at", "244969_at", "244970_at", + "244971_at", "244972_at", "244973_at", "244974_at", "244975_at", + "244976_at", "244977_at", "244978_at", "244979_at", "244980_at", + "244981_at", "244982_at", "244983_at", "244984_at", "244985_at", + "244986_at", "244987_s_at", "244988_s_at", "244989_s_at", "244990_s_at", + "244991_s_at", "244992_s_at", "244993_s_at", "244994_at", "244995_at") selected<-mget(c("244901_at", "244910_s_at", "245000_at", "245001_at", "245002_at", + "245003_at", "245004_at", "245005_at", "245006_at", "245007_at", + "245008_at", "245009_at", "244911_at", "245010_at", "245011_at") params <- new("GOHyperGParams", geneIds = selected, universeGeneIds = universe, annotation="ath1121501", + ontology = "MF", pvalueCutoff = 0.5, conditional = FALSE, testDirection = "over") hgOver <- hyperGTest(params) head(summary(hgOver), n = 1) GOMFID Pvalue OddsRatio ExpCount Count Size Term 1 GO:0005488 0.006822516 2.87234 20.08571 27 38 binding The above works but when I intend to use it for the whole data as follows it fails: universe <- unlist(mget(myd, ath1121501ACCNUM)) Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : value for "245651_s_at" not found length(as.list(toggleProbes(ath1121501ACCNUM,"all"))) [1] 22809 # whereas there should be 22810 as in the chip. -- output of sessionInfo(): R version 2.15.2 (2012-10-26) Platform: i686-redhat-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] annaffy_1.28.0 KEGG.db_2.7.1 GO.db_2.7.1 GOstats_2.22.0 graph_1.34.0 [6] Category_2.22.0 ath1121501.db_2.7.1 org.At.tair.db_2.7.1 RSQLite_0.10.0 DBI_0.2-5 [11] AnnotationDbi_1.18.4 BiocInstaller_1.4.9 limma_3.12.3 affy_1.34.0 Biobase_2.16.0 [16] BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affyio_1.22.0 annotate_1.34.1 genefilter_1.38.0 GSEABase_1.18.0 [5] IRanges_1.14.4 preprocessCore_1.18.0 RBGL_1.32.1 splines_2.15.2 [9] stats4_2.15.2 survival_2.36-14 tools_2.15.2 XML_3.9-4 [13] xtable_1.6-0 zlibbioc_1.2.0 -- Sent via the guest posting facility at bioconductor.org.