[BioC] Problem with the oligo package for nimblegen analysis

[William Oldham]

I am by no means an expert, but ran across your post as I encountered the same
 problem. While I was not able to fix it, I was able to find a work-around 
by writing the phenodata to the expressionset after reading in the files.  
I suspect the following would work in this case as well:

maqc <- read.xysfiles(xys.files)
phenoData(maqc) <- pd

I hope this works to get you through the example and hopefully someone 
more knowledgeable about the Biobase changes that result in this error 
will respond as well.

Best,

Will