Entering edit mode
Paolo Kunderfranco
▴
350
@paolo-kunderfranco-5158
Last seen 7.2 years ago
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