Dear Geoff,

When you open your "**FinalReport.txt" file using any text editor, do you
see [Header] in the first line, and [Sample Methylation Profile] in about
the 8th line?  Also check if there are extra blanks at the end of the first
several lines.  Sometimes the extra blanks will mess up the reading.

To convert MethyLumiSet to MethyLumi, you can try this:
new_MethyLumi_data <- as(old_MethyLumiSet_data, "MethyLumi")

Wei

	[[alternative HTML version deleted]]

