Hi all,

I am very new to microarray analysis and bead arrays so please excuse me if this is a silly question.  I am attempting to associated the gene file for Mouse Ref 6 V1.1.  I am using the following code to load the summary file but I am unable to access the ProbeID information. 

c.names=list(exprs = "AVG_Signal", NoBeads = "Avg_NBEADS", Detection="Detection", se.exprs ="BEAD_STDEV" ,Narrays="NARRAYS", arrayStDev = "ARRAY_STDEV")
BSData = readBeadSummaryData(dataFile,skip=7, ProbeID="TargetID", columns=c.names)
library(illuminaMousev1p1)
illuminaMousev1p1()
ids = rownames(exprs(BSData))
chr = mget(ids, illuminaMousev1p1CHR,ifnotfound = NA)
chrloc = mget(ids, illuminaMousev1p1CHRLOC,ifnotfound = NA)
refseq = mget(ids, illuminaMousev1p1REFSEQ,ifnotfound = NA)
genename = mget(ids, illuminaMousev1p1GENENAME,ifnotfound = NA)
anno = cbind(Ill_ID = as.character(ids), Chr = as.character(chr), Loc = as.character(chrloc), RefSeq = as.character(refseq), Name = as.character(genename))
ebFit$genes = anno
topTable(ebFit)

R version 2.6.0 (2007-10-03) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] illuminaMousev1p1_1.2.0 lumi_1.4.0              mgcv_1.3-27             beadarray_1.6.0         affy_1.16.0             preprocessCore_1.0.0   
 [7] affyio_1.6.1            geneplotter_1.16.0      lattice_0.16-5          annotate_1.16.1         xtable_1.5-2            AnnotationDbi_1.0.6    
[13] RSQLite_0.6-3           DBI_0.2-4               Biobase_1.16.1          limma_2.12.0            gplots_2.3.2            gdata_2.3.1            
[19] gtools_2.4.0           

loaded via a namespace (and not attached):
[1] grid_2.6.0         KernSmooth_2.22-21 RColorBrewer_1.0-2


 When I use the "ids = rownames(exprs(BSData))" command the information I get is the row number not the ProbeID.  Am I doing something incorrectly?  Any help would be very much appreciated.

Thank you,
Cherie



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