[BioC] NA geneSymbol with lumi

Sebastien Gerega seb at gerega.net
Fri Nov 9 04:36:14 CET 2007


Hi,
I am using the lumi package to analyse illumina microarray data.
When it finally comes to getting the top 10 DE genes with topTable I get 
many hits with
the geneSymbol <NA>. However, if I look up the ProbeID corresponding to 
the nuID
that provide <NA>, I find that they do correspond to genes. Why aren't 
they being
displayed in the topTable?
thanks,
Sebastien

                      ID geneSymbol     logFC         t      P.Value    
adj.P.Val        B
1917  fwfUovXT3rjAjqbpJU     S100A8 -5.307223 -50.43759 9.854174e-09 
0.0001383625 8.724832
12632 Qd_S7V4OkLjsX3jkt4      KRT6B -5.281406 -39.54237 3.896317e-08 
0.0002735409 8.229157
12149 BjSTT6BOqGLhpKKFGI       <NA> -3.118669 -30.01505 1.844180e-07 
0.0008631377 7.451766
7474  6ipCUUDxcp4ryIj6Uk       <NA> -3.155916 -24.45685 5.835502e-07 
0.0013366890 6.716048
3831  3nivfFfvk55Rd18lLk       <NA> -2.690362 -24.10891 6.324511e-07 
0.0013366890 6.659617



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