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 >

Hi Paolo, There are many reasons why some probes may not match up to a gene symbol. Sometimes the probe was designed to a gene region that is poorly studies and does not yet have an official gene symbol, and sometimes the probe was designed to sequence that later was found to not really match to a gene (in this case the probe will not map to anything at all). In the case of the probe below (oii7mSFyrr_AMWODH0), this seems to be the latter case since I cannot even get an entrez gene ID for this probe. library(lumiMouseAll.db) select(lumiMouseAll.db, keys=k, cols=c("SYMBOL","GENENAME","ENTREZID"), keytype="PROBEID") Marc On 07/30/2012 09:13 AM, Paolo Kunderfranco wrote: > 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 > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor