[BioC] Time course....makeConstrasts()

[Khan, Sohail]

Dear all,

I have an Affy time course experiment as follows:
0hr - 2hr - 4hr, I have 2 replicates for the 2hr and 4hr and only one (chip) for 0hr.  Would I be able to analyze this experiment using limma? (I know its not a good idea).
Actually I tried analyzing this in limma, and got the following error when constructing contrasts:
Error in parse(file, n, text, prompt) : parse error
I am assuming this is due to the design matrix having only one chip for the 0hr time point.  Thanks for your suggestions/advice. 



Sohail Khan
Scientific Programmer
COLD SPRING HARBOR LABORATORY
Genome Research Center
500 Sunnyside Boulevard
Woodbury, NY 11797
(516)422-4076