[BioC] Reading Illumina data from GenomeStudio in limma

[Josh [guest]]

I have data exported from GenomeStudio (1.6) that I can correctly read and pre-process with lumi. However, when I try using read.ilmn in limma, I found that I get an error saying "Error in `rownames<-`(`*tmp*`, value = list(PROBE_ID = c("ILMN_1762337",  : length of 'dimnames' [1] not equal to array extent." I have found that this was due to the inclusion of extra columns in my probe profiles (TargetID, ProbeID, SPECIES, SOURCE, TRANSCRIPT and on). When I removed them, I can correctly read the probe and control profiles with read.ilmn. Is there a better fix around this than manually removing the columns?

 -- output of sessionInfo(): 

R version 3.0.0 (2013-04-03)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] lumi_2.12.0        Biobase_2.20.0     BiocGenerics_0.6.0 limma_3.16.2

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