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