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
most of them (around 10%)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

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