Hi

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' [1] 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! 

It's hard to give any help with so little information from you. The error message can come from many causes, and your problem does not appear to be similar to that in the previous post you link to.

What do you mean by "the control probes are in a table"? What control probe file do you actually have and where did you get it from? What limma function did you use to try to read the control probe file?

What are the "two matrices" that you refer to, and how could they have different columns if they are supposed to relate to the same biological samples?

Where are you getting the Illumina expression data from? Do you have access to the Illumina raw data including the idat files?