Hi all, Do you think it is good to normalize two illumina chips (done months apart) together? Or do I normalize the chips separately? Any suggestions would be very helpful Thanks Yogi [[alternative HTML version deleted]]

On Thu, May 29, 2008 at 2:53 AM, Yogi Sundaravadanam <yogi.sundaravadanam at="" agrf.org.au=""> wrote: > Hi all, > > > > Do you think it is good to normalize two illumina chips (done months > apart) together? Or do I normalize the chips separately? Generally, it is a good idea to normalize together when you can. You will want to do some QC before you can make a decision, though. Sean

Dear Yogi: I think you should do the normalization for the two chips instead of normalizing them separately. Given the two chips were hybridized at different time, I would expect there is obvious difference between the two chips (you can check this using boxplot). The between-array normalization across the two chips can help remove this difference. Hope this helps. Cheers, Wei Yogi Sundaravadanam wrote: > Hi all, > > > > Do you think it is good to normalize two illumina chips (done months > apart) together? Or do I normalize the chips separately? > > > > Any suggestions would be very helpful > > > > Thanks > > Yogi > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >