[BioC] read.ilmn error: length of 'dimnames' [1] not equal to array extent

[Mark Ebbert]

Hi,

This is my first time analyzing Illumina microarray data, so I'm not familiar with the data format as exported by BeadStudio or GenomeStudio. The problem is that I can't get read.ilmn to read in either the sample data or the control data. The error I get when reading in the sample data alone is as follows:

Error in `rownames<-`(`*tmp*`, value = list(PROBE_ID = c("ILMN_2896528",  : 
  length of 'dimnames' [1] not equal to array extent

When reading in the control data I get the following error:

Error in readGenericHeader(fname, columns = expr) : 
  Specified column headings not found in file

This data comes from the Genome Technology Access Center at WashU and they claim the data is directly exported from GenomeStudio.

Could it be from unexpected characters in the file (e.g. R doesn't like #, -, and other characters in certain situations)? There aren't any #'s in the file, but I'm curious is read.ilmn handles these cases. The sample names do have '-' in the name, but I tried removing those and it didn't make a difference.

I appreciate your help!

Mark