[BioC] lumi - limma - geneSymbol/geneName

[Paolo Kunderfranco]

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
>