I am very new to processing and analyzing microarray data so forgive me if my question isn't well formulated. I have pre-processed and normalized my microarray data (Affymetrix U133a) so now I have 1 file containing normalized values with gene names in the rows and samples in the columns. The data consists of 8 subjects with expression taken at two time points (before and after sleep deprivation). I also have covariate data consisting of dichotomized results (0/1 pass/fail) from various neuropsychological tests that were administrated before and after sleep deprivation.
I am trying to find genes/gene clusters that are associated with sleep deprivation. I have looked numerous times at the limma userguide for guidance on how to set up my analysis, but haven't been able to figure this out.
Any guidance would be very appreciated. Thank you.