Dear All, I am working with lumi / limma package to detect differentially expressed genes between two or more samples, I was wondering why when I add geneSymbol and geneName to my Illumina probelist some of them are not called and remained NA, for instance (last row): if (require(lumiMouseAll.db) & require(annotate)) { geneSymbol <- getSYMBOL(probeList, 'lumiMouseAll.db') geneName <- sapply(lookUp(probeList, 'lumiMouseAll.db', 'GENENAME'), function(x) x[1]) fit1_2$genes <- data.frame(ID= probeList, geneSymbol=geneSymbol, geneName=geneName, stringsAsFactors=FALSE) } 7671 69fpKOOuFduFbAjNVU Dppa5a developmental pluripotency associated 5A 7.828381 9.333743 149.31710 2.773571e-18 6.144846e-14 29.80858 16014 QpWgiAmByT4gW7iui0 Pou5f1 POU domain, class 5, transcription factor 1 5.305532 8.633706 103.85793 1.098423e-16 8.143726e-13 27.72832 20450 HlUzpCHheswfSZNdQo Trh thyrotropin releasing hormone 5.603441 8.761965 103.81774 1.102739e-16 8.143726e-13 27.72571 7670 o7Ah_nzF7JdZOTtd9U Dppa4 developmental pluripotency associated 4 5.300619 8.626239 99.82457 1.640729e-16 9.087587e-13 27.45790 7672 xjn0tTp4isUXmUkAKI Dppa5a developmental pluripotency associated 5A 7.663922 9.439668 97.09091 2.173661e-16 9.631491e-13 27.26346 17719 ZXvxHuC6s3xogRFJfo Sall4 sal-like 4 (Drosophila) 4.456642 8.585243 90.39110 4.484584e-16 1.655932e-12 26.74469 14084 06jqfFxe5_X97NRXuk Myl3 myosin, light polypeptide 3 -7.736059 13.128014 -88.39591 5.622067e-16 1.779384e-12 26.57755 8757 oii7mSFyrr_AMWODH0 <na> <na> 4.608167 8.438770 78.65631 1.833459e-15 5.077535e-12 25.66512 any ideas? thanks paolo > sessionInfo() R version 2.15.0 (2012-03-30) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252 [3] LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C [5] LC_TIME=Italian_Italy.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] lumiMouseIDMapping_1.10.0 lumi_2.8.0 [3] BiocInstaller_1.4.7 lumiMouseAll.db_1.18.0 [5] org.Mm.eg.db_2.7.1 RSQLite_0.11.1 [7] DBI_0.2-5 AnnotationDbi_1.18.1 [9] limma_3.12.1 nleqslv_1.9.3 [11] methylumi_2.2.0 ggplot2_0.9.1 [13] reshape2_1.2.1 scales_0.2.1 [15] Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affy_1.34.0 affyio_1.24.0 annotate_1.34.1 [4] bigmemory_4.2.11 Biostrings_2.24.1 bitops_1.0-4.1 [7] BSgenome_1.24.0 colorspace_1.1-1 dichromat_1.2-4 [10] digest_0.5.2 DNAcopy_1.30.0 GenomicRanges_1.8.9 [13] genoset_1.6.0 grid_2.15.0 hdrcde_2.16 [16] IRanges_1.14.4 KernSmooth_2.23-8 labeling_0.1 [19] lattice_0.20-6 MASS_7.3-19 Matrix_1.0-7 [22] memoise_0.1 mgcv_1.7-19 munsell_0.3 [25] nlme_3.1-104 plyr_1.7.1 preprocessCore_1.18.0 [28] proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.91-1.1 [31] Rsamtools_1.8.5 rtracklayer_1.16.3 stats4_2.15.0 [34] stringr_0.6.1 tools_2.15.0 XML_3.9-4.1 [37] xtable_1.7-0 zlibbioc_1.2.0