[BioC] print layout for Agilent data?

[Jianping Jin]

Dear list,

When I was trying the normalizeWithinArrays function of limma I got an 
error: Error in switch (method, loess = {: Layout argument not specified). 
I was using an Agilent 4 x 44k data set and knew the Agilent printer has 
only one block (Row and Col having been taken already). How can I do loess 
normalization for each slide? Should I add a Block column into the RG, the 
data read-in file in order to do normalizaWithinArrays?

Another question is that is there any easy way I can remove all control 
spots from all data files?

Appreciate your help!

JJ

##################################
Jianping Jin Ph.D.
Bioinformatics scientist
Center for Bioinformatics
Room 3133 Bioinformatics building
CB# 7104
University of Chapel Hill
Chapel Hill, NC 27599
Phone: (919)843-6105
FAX:   (919)843-3103
E-Mail: jjin at email.unc.edu