[BioC] lumi - limma - geneSymbol/geneName

[Marc Carlson]

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
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