[BioC] #Identify differentially expressed genes

Gordon K Smyth smyth at wehi.EDU.AU
Fri Aug 24 06:56:33 CEST 2012

Dear Paolo,

An alternative is to use the gene symbols from the Illumina manifest file. 
The gene symbols are often included in the probe summary profile files 
output by BeadStudio or GenomeStudio, and are read in automatically by the 
read.ilmn() function of the limma package.  See the "Mammary Progenitor 
Cell Populations" case study in the limma User's Guide for a fully worked 

Of course not all probes have gene names, no matter what annotation you 

Best wishes

--------------- original message --------------
[BioC] #Identify differentially expressed genes
Paolo Kunderfranco paolo.kunderfranco at gmail.com
Thu Aug 23 12:26:51 CEST 2012

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 
most of them (around 10%)are not called and remained NA, for instance 

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
16014 QpWgiAmByT4gW7iui0     Pou5f1 POU domain, class 5, transcription
factor 1  5.305532  8.633706 103.85793 1.098423e-16 8.143726e-13
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
7672  xjn0tTp4isUXmUkAKI     Dppa5a    developmental pluripotency
associated 5A  7.663922  9.439668  97.09091 2.173661e-16 9.631491e-13
17719 ZXvxHuC6s3xogRFJfo      Sall4                     sal-like 4
(Drosophila)  4.456642  8.585243  90.39110 4.484584e-16 1.655932e-12
14084 06jqfFxe5_X97NRXuk       Myl3                 myosin, light
polypeptide 3 -7.736059 13.128014 -88.39591 5.622067e-16 1.779384e-12
8757  oii7mSFyrr_AMWODH0       <NA>
     <NA>  4.608167  8.438770  78.65631 1.833459e-15 5.077535e-12

any ideas?

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