I'm trying to analyse some microarray data using Limma. The sample probe data is in GenomeStudio format and Limma read this nicely, but the control probes are in a table.
When I load this into Limma I got an error:
Error in readGenericHeader(fname, columns = expr, sep = sep) :
Specified column headings not found in file
After some search, I found a post that deals with a similar problem: read.ilmn error: length of 'dimnames'  not equal to array extent but I can't merge the two matrices since the number of columns is totally different.
Any idea on how one can get around this issue?
Thanks in advance!