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Dear Erika, thank you! The more precise question makes it much easier to give a useful answer :) * for normalization, consider quantile normalization (in limma) or vsn (either through that package directly or via limma) * for quality assessment, consider the arrayQualityMetrics package (see http://www.microarray-quality.org/quality_metrics.html - for using it with one color data, you need to provide them in the form of an ExpressionSet). * for differential expression with empirical Bayes, limma. Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber Erika ha scritto: > Dear Wolfgang, > > My apologies, I'll try to make my question more precise. I've got a table > with intensity raw data and flag data obtained from 14 codelink arrays, each > one from a distinct sample, from two categories. I'd like to know how I > could normalize this data and find differentiatly expressed genes. > With affy array data, I used to run rma and mas5, and then run empirical > bayes to find differentiatly expressed genes. > I hope I made my point clear. > > Best wishes > > Erika > > 2007/11/28, Wolfgang Huber <huber at="" ebi.ac.uk="">: >> Dear Erika, >> >>> I'm a newbie to bioconductor, but I've already done some analysis an >> affy >>> arrays. However, I've got some data obtained in the codelink system that >> I'd >>> like to analyze in bioconductor as well. What packages should I use? Can >>> affy packages be used for these data? >> Please have a look at the limma package. >> >> You might also try to formulate your question more precisely. "analyse" >> is a fairly unspecific task description, almost all of the packages on >> Bioconductor can be used for some kind of analysis or other. >> >> Best wishes >> Wolfgang >> >> ------------------------------------------------------------------ >> Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >>