While I cannot recall the details there has been some discussion of this on the email list. Search the archives especially wrt. posts from the maintainer of GCRMA, Zhijin Wu Kasper On Dec 22, 2008, at 22:59 , Wen Huang wrote: > I have more information on this question: > > I was able to access previous version of R2.7.2/BioConductor2.2 and > used the same code in the vignette of "gcrma" with the "Dilution" > data, the expression values were different between versions of R/BioC. > > Anybody knows anything about it? > > Thank you, > Wen > > Begin forwarded message: > >> From: Wen Huang <whuang.ustc at="" gmail.com=""> >> Date: December 22, 2008 1:18:29 PM CST >> To: bioconductor at stat.math.ethz.ch >> Subject: discrepancies using different gcRMA >> >> Hi, >> >> I have a question about the difference between different versions of >> gcRMA. >> >> I recently (a couple weeks ago) updated R and Bioconductor and tried >> to reproduce some analysis I have done back in the summer. I found >> that the expression values I got using simply the function "gcrma()" >> were different. I checked the documentation and it says a few >> options were added but not really helpful to my question. >> >> I just wonder if anybody knows a quick way to add some options to >> the new version of gcRMA and reproduce what the old gcRMA did before. >> >> Thanks a lot, >> Wen > > > [[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