jim, thanks much for the response. well, a definitive answer, even if it's not the one you're looking for, is better than a vague answer or no answer at all. given what appears to be a good deal of work involved in going the gcrma() route, with no guarantee of success, it seems pretty clear that using rma() is the way to go. in fact, i just ran rma() on an affy batch object returned by combineAffyBatch() that contains data from 40 chips - 25 from mouse 430a and 15 from mouse 430_2, and it ran without error. i'm happy. thanks again, mike Michael Palumbo palumbo at wadsworth.org Bioinformatics Core TGI/RTP & VM: (518) 880-1360 Wadsworth Center CMS: (518) 402-4587 Center for Medical Science New York State Dept of Health 150 New Scotland Ave Albany, NY 12208 James W. MacDonald wrote: > Hi Michael, > > Michael Palumbo wrote: >> hello, >> >> i'm new to bioconductor and processing array data, but i'm not new to >> R - not an expert, either, let's say mildly competent... >> >> (output of sessionInfo() is at bottom of this email.) >> >> the short version of my question: >> i'm having trouble running gcrma() on an affy batch object returned >> from combineAffyBatch(). the combined object is created by combining >> data from two types of mouse chips: moe430a and mouse4302. gcrma() >> returns this error: >> >> > gcrma.eset.A.V2 <- gcrma(comb.A.V2$dat) >> >> Adjusting for optical effect...Done. >> >> Computing affinitiesError in getCDF(cdfpackagename) : The current >> operation could not access the Bioconductor repository. Please check >> your internet connection, and report further problems to >> bioconductor at stat.math.ethz.ch >> >> >> the long version of my question, and more code: >> i believe the combining of chip data occurs without error. i put the >> newly computed cdf in the global environment - i think this is where >> the problem is - like it's not being recognized. > > So there are two problems here. First, getCDF() looks for an > _installed_ cdf package, rather than an environment, and if it doesn't > find the installed package it tries to get one from BioC, which as you > know is failing. I could envision some sort of hackery that could get > around this problem. However... > > The second problem is that you don't have a probe package that > corresponds to the cdf you are using. Without the probe package you > will not be able to proceed anyway, so the first point is sorta moot. > > If you are really wedded to the idea of using gcrma(), I suppose you > could get the probe_tab files for each of the chips you are using > (from the Affy website), use awk or Perl or some such to come up with > a combined probe_tab file that would correspond to the combined cdf > that you are using, build the probe package, do some hack to getCDF() > to find the cdfenv and then proceed happily. > > Or else you could forget all that stuff, do RMA on your data, and > proceed (slightly less) happily, but without spending all the time > required to do the above. > > Unless there is some obvious solution that escapes me. There are > others here who use gcrma() all the time who may have already met and > surmounted this problem. Although, as you noted, nobody is talking > about it ;-D. > > Sorry I can't be more helpful... > > Best, > > Jim > > >> >> >>> library(mouse4302cdf) >> >> >>> library(moe430acdf) >> >> >>> comb.A.V2 <- combineAffyBatch(list(A,V2),c("moe430aprobe", >> >> "mouse4302probe"),newcdf="comb.430a.4302.cdf") >> >> package:moe430aprobe moe430aprobe >> package:mouse4302probe mouse4302probe >> 245487 unique probes in common >> >> # put new cdf in global environment >> >> >>> comb.430a.4302.cdf <- comb.A.V2$cdf >> >> >>> library(gcrma) >> >> >> Loading required package: splines >> >> >>> gcrma.eset.A.V2.3 <- gcrma(comb.A.V2$dat) >> >> >> Adjusting for optical effect...Done. >> >> Computing affinitiesError in getCDF(cdfpackagename) : The current >> operation could not access the Bioconductor repository. Please >> check your internet connection, and report further problems to >> bioconductor at stat.math.ethz.ch >> >> ------ >> when i check the cdf of the combined object, it looks correct to me: >> >> >> >>> cdfName(comb.A.V2$dat) >> >> >> [1] "comb.430a.4302.cdf" >> >> >> -------------------- >> >> > sessionInfo() >> R version 2.4.1 (2006-12-18) >> i386-pc-solaris2.10 >> >> locale: >> /en_US.ISO8859-1/C/C/en_US.ISO8859-1/en_US.ISO8859-1/C >> >> attached base packages: >> [1] "splines" "tools" "stats" "graphics" "grDevices" >> "utils" [7] "datasets" "methods" "base" >> other attached packages: >> hgu95av2probe hgu95av2cdf hgu95acdf mouse4302probe >> moe430aprobe >> "1.0" "1.4.3" "1.4.1" "1.14.0" >> "1.14.0" >> gcrma moe430acdf mouse4302cdf matchprobes >> affy >> "2.6.0" "1.14.0" "1.14.0" "1.6.0" >> "1.12.2" >> affyio Biobase >> "1.2.0" "1.12.2" >> >> i've searched the email list (what i think is) extensively and >> although i've found other mentions of similar problems i haven't >> stumbled across a solution that works for me. in particular, i tried >> a fairly different approach that involved creating affinity info >> objects and that didn't work either (i can supply the error of that >> attempt if necessary). the method i tried is described here >> <http: thread.gmane.org="" gmane.science.biology.informatics.conducto="" r="" 2500="" focus="2747">. >> >> >> thanks in advance for any and all help, >> mike >> > >