Dear Bioconductor people, I am trying to reproduce a microarray analysis from the publicly available raw data of a publication. The pre-processing method is detailed in the Methods (robust multi- array analysis with quantile normalization) and I have used the rma function with the appropriate 'normalize' option. However this yields results similar to those published but not quite the same values. I was wondering if this could come from the version of my affy package (current bioconductor package version): the authors in the publication used affy package v1.5.8. However, the 1.5.8 is not available to download anymore (BioC v1.5 is not online anymore). Maybe someone still has the sources? Thank you very much in advance for your help. Best regards, Leonor Palmeira.

Hi Leonor, Leonor Palmeira wrote: > Dear Bioconductor people, > > I am trying to reproduce a microarray analysis from the publicly > available raw data of a publication. > > The pre-processing method is detailed in the Methods (robust multi- array > analysis with quantile normalization) and I have used the rma function > with the appropriate 'normalize' option. However this yields results > similar to those published but not quite the same values. > > I was wondering if this could come from the version of my affy package > (current bioconductor package version): the authors in the publication > used affy package v1.5.8. However, the 1.5.8 is not available to > download anymore (BioC v1.5 is not online anymore). Maybe someone still > has the sources? Actually yes. Nothing ever goes away. And if I am not mistaken, you can get this for yourself. All you need is a subversion client, which you can get here if you aren't on Linux (if you are on Linux it is easier to install using whatever package manager your distro uses): http://subversion.tigris.org/ Then you can get any of the packages from release 1.5 here: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_1_5/madman/Rp acks e.g., svn co https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_1_5/madman/Rp acks/affy will get you the affy sources. You want to use the username readonly and password readonly, which I think should work. You will probably need to get other packages as well, depending on what the dependencies were for affy at that time. In addition, you will need to get R-2.0.0, as there is no guarantee that an old affy will run on current R. You might also just try installing R-2.0.0 and running biocLite(). It might actually work. Best, Jim > > Thank you very much in advance for your help. > Best regards, > Leonor Palmeira. > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662