Hi, I have been searching information on 'minfi', but haven't found any except that it's used to analyze Illumina 450k data and it does something similar to what Genome Studio does (which I'm not familiar with). I used methylumi earlier, and normalizing with minfi, I find that normalization outputs are quite different, especially if I plot betas for design I and II probes separately. It would be good to know what minfi actually does. Also, does minfi being born make methylumi deprecated? Cheers, Khadeeja [[alternative HTML version deleted]]

Hi Khadeeja, Have you seen the minfi vignette ...? http://bioconductor.org/packages/2.10/bioc/html/minfi.html It's quite comprehensive and Section 4 specifically addresses normalization. Kasper is the authority on this, I've cc'd him on the message. Valerie On 12/16/2011 09:18 AM, khadeeja ismail wrote: > Hi, > > I have been searching information on 'minfi', but haven't found any except that it's used to analyze Illumina 450k data and it does something similar to what Genome Studio does (which I'm not familiar with). > I used methylumi earlier, and normalizing with minfi, I find that normalization outputs are quite different, especially if I plot betas for design I and II probes separately. > > It would be good to know what minfi actually does. > > > Also, does minfi being born make methylumi deprecated? > > Cheers, > Khadeeja > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]