Dear Jim Thank you for mentioning xps as one of the available options for exon arrays. Regarding the memory needed, xps needs machines with 1 GB RAM only. I have tested this with HuExon arrays for Windows XP, Mac OS X and Linux. Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._ James W. MacDonald wrote: > Hi Jennifer, > > Barb, Jennifer (NIH/CIT) [E] wrote: >> Hello All, I am fairly new to processing exon array CEL files using >> the Affy package in Bioconductor and I was trying to obtain RMA >> values for 6 chips on the Human Exon 1.0 st array and I received the >> following error message after the rma command was run: >>> eset<-rma(data) > > The affy package is not designed to work with the exon arrays. There > are three packages designed to analyze these arrays; oligo, xps, and > exonmap. I just wrote a blurb that will (or maybe has) appear on the > BioC website, showing what is required for such things. The relevant > portion looks like this: > > Affymetrix Exon ST Arrays: > > oligo > - Requires a pdInfoPackage built using pdInfoBuilder > - This package collates cdf, probe, annotation data together > - These packages are available from Bioconductor via biocLite() > > exonmap > - Requires installation of MySQL and Ensembl core database tables > - Requires specially modified cdf (available at > http://xmap.picr.man.ac.uk/download/) and affy package > > xps > - Requires installation of ROOT > - Uses data files from Affymetrix (.CDF, .PGF, .CLF, .CSV) directly > > The part about the pdInfoPackage being available appears not to be > quite true as yet. We built them, but there were a couple of technical > aspects that need to get fixed before they will be downloadable via > biocLite(). And I have no idea how long that might take, although if > Marc Carlson sees this he may chime in. > > In the interim you could build your own using pdInfoBuilder. However, > for the exon arrays you will need a 64-bit linux box with something > like 8 Gb RAM to use either oligo or exonmap, due to the amount of > memory these things require. You might be able to use xps on Windows > with say 4 Gb RAM, but I am not sure about that. > > Another R solution is aroma.affymetrix which has its own mailing list > - you can google to find more information about that. > > Best, > > Jim > > >> >> Error in getCdfInfo(object) : Could not obtain CDF environment, >> problems encountered: Specified environment does not contain >> HuEx-1_0-st-v2 Library - package huex10stv2cdf not installed >> Bioconductor - could not connect In addition: Warning message: In >> readLines(biocURL) : cannot open: HTTP status was '503 Service >> Unavailable' >> >> I am under the impression that exon arrays have different library >> files than the traditional cdf files used for the IVT expression >> arrays. The 4 library files for the exon array exist with the >> following extensions: .mps, .clf, .pgf, .qcc. Is there something >> special needed for processing exon arrays in bioconductor? Thank you, >> Jennifer >> >> >> [[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 >