A fourth one could be to use ComBat: http://jlab.byu.edu//ComBat/Abstract.html G --------------------------------------------------------- Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiveld at wur.nl internet: http://nutrigene.4t.com http://www.researcherid.com/rid/F-4912-2010 -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of Wolfgang Huber Sent: Monday, September 26, 2011 10:48 To: bioconductor at r-project.org Subject: Re: [BioC] right normalization? Dear Andrea I see three options, in order of complexity: - add a 'batch' factor into the linear model that you fit with limma in order to absorb the batch effect - do the limma analysis separately for both batches, then combine afterwards - use the 'sva' package. http://www.biostat.jhsph.edu/~jleek/sva/index.html Best wishes Wolfgang Sep/26/11 10:29 AM, andrea.grilli at ior.it scripsit:: > Hi list, > I've got 16 gene chip affymetrix arrays of 2 cell lines at different > time/conditions. Chips were done in 2 different moments, and this bias > seems to affect my analysis. > > I've normalized with RMA and analyzed with eBayes models to compare > the 2 cell lines at each time point. > Following analysis are affected by the above mentioned "time bias", > like in clustering were data are grouped according to when the arrays > were hybridized. > > - Do you suggest a different normalization? Which one could reduce > this effect? > > - could be a good approach normalizing the 2 groups of samples > separately (will be 8 and 8) and merging the data after normalization? > > > I did quality control steps like in bioconductor book, and all > parameters are in the right ranges. Also box plot shows a similar > expression range across samples. > Any help will be really appreciated, > thanks in advance, > > Andrea > > > > PS This is a semplification of a previous mail, sorry for the repetition. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor