Dear list, I would like to do an analysis on a published dataset that used the "previous generation" (quote Affy) arrays Mu11K. These contain ~11K probes divided over 2 chips, give rise to 2 cel files, and use different annotation packages. As I am no limma-veteran, I wondered if there was a way to concatenate the data from these files before or after reading it into limma as two separate affybatch objects, and then make an eSet. If not, should I instead analyse the chips separately and merge the resulting toptables? cheers, -- Jorrit Boekel Ph.D. student Dept. of Neuroscience Karolinska Institute Stockholm, Sweden

Jorrit Boekel ha scritto: > Dear list, > > I would like to do an analysis on a published dataset that used the > "previous generation" (quote Affy) arrays Mu11K. These contain ~11K > probes divided over 2 chips, give rise to 2 cel files, and use different > annotation packages. > > As I am no limma-veteran, I wondered if there was a way to concatenate > the data from these files before or after reading it into limma as two > separate affybatch objects, and then make an eSet. If not, should I > instead analyse the chips separately and merge the resulting toptables? > > cheers, Dear Jorrit it is better to do the normalisation and quality control separately. For whether you then merge pre or post differential expression analysis with limma, I don't see any big concerns either way, that is probably more a question of what you find more convenient. Best wishes Wolfgang ------------------------------------------------ Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber