Hello, I am trying to process some CEL files using the affy package in Bioconductor. I am using the steps given in the Bioconductor manual given here - http://manuals.bioinformatics.ucr.edu/home/R_BioCondManua l#biocon_affypack Here is the list of commands I used: mydata <- ReadAffy(cdfname = "hugene10stv1.r3cdf") > eset <- rma(mydata) Background correcting Normalizing Calculating Expression > eset_PMA <- mas5calls(mydata) Getting probe level data... Computing p-values Error in FUN(1:10[[1L]], ...) : NA/NaN/Inf in foreign function call (arg 2) So, I am getting an error in the mas5calls function. Here is the sessionInfo(): R version 2.10.1 (2009-12-14) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hugene10stv1.r3cdf_2.5.0 affy_1.24.2 [3] Biobase_2.6.1 loaded via a namespace (and not attached): [1] affyio_1.14.0 preprocessCore_1.8.0 tools_2.10.1 And here is the traceback(): 7: .C("DetectionPValue", as.double(pms[, x]), as.double(mms[, x]), as.character(pns), as.integer(length(mms[, x])), as.double(tau), as.double(sat), dpval = double(length(unique.pns)), length(unique.pns), PACKAGE = "affy") 6: FUN(1:10[[1L]], ...) 5: lapply(X, FUN, ...) 4: sapply(1:length(pms[1, ]), function(x) { .C("DetectionPValue", as.double(pms[, x]), as.double(mms[, x]), as.character(pns), as.integer(length(mms[, x])), as.double(tau), as.double(sat), dpval = double(length(unique.pns)), length(unique.pns), PACKAGE = "affy")$dpval }) 3: mas5calls.AffyBatch(object, ...) 2: mas5calls(mydata) 1: mas5calls(mydata) Kindly let me know if I am missing something, or whether it is possible that there is something wrong with the data. I tried using the "Dilution" dataset, and it seems to work. Thanks in advance. Warm Regards Karthik Ramaswamy Padmanabhan M.S in Bioinformatics Indiana University, Bloomington [[alternative HTML version deleted]]

Dear Karthik, Please note that the Affymetrix MAS5 algorithm requires both PM and MM values, and the HuGene (and HuExon) arrays do not have MM values. For this reason the "affy" package cannot run mas5calls for HuGene arrays. As a note, my package "xps" allows to do mas5 and mas5.call for HuGene and HuExon arrays. However, I would not recommend to use mas5.call for HuGene but use dabg.call, which is the algorithm Affymetrix has developed for HuGene/HuExon arrays and which is also available in xps. Best regards 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 _._._._._._._._._._._._._._._._._._ Karthik Ramaswamy Padmanabhan wrote: > Hello, > > I am trying to process some CEL files using the affy package in Bioconductor. I am using the steps given in the Bioconductor manual given here - http://manuals.bioinformatics.ucr.edu/home/R_BioCondManua l#biocon_affypack > > Here is the list of commands I used: > > mydata <- ReadAffy(cdfname = "hugene10stv1.r3cdf") > >> eset <- rma(mydata) >> > Background correcting > Normalizing > Calculating Expression > >> eset_PMA <- mas5calls(mydata) >> > Getting probe level data... > Computing p-values > Error in FUN(1:10[[1L]], ...) : > NA/NaN/Inf in foreign function call (arg 2) > > So, I am getting an error in the mas5calls function. Here is the sessionInfo(): > > R version 2.10.1 (2009-12-14) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hugene10stv1.r3cdf_2.5.0 affy_1.24.2 > [3] Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 preprocessCore_1.8.0 tools_2.10.1 > > And here is the traceback(): > > 7: .C("DetectionPValue", as.double(pms[, x]), as.double(mms[, x]), > as.character(pns), as.integer(length(mms[, x])), as.double(tau), > as.double(sat), dpval = double(length(unique.pns)), length(unique.pns), > PACKAGE = "affy") > 6: FUN(1:10[[1L]], ...) > 5: lapply(X, FUN, ...) > 4: sapply(1:length(pms[1, ]), function(x) { > .C("DetectionPValue", as.double(pms[, x]), as.double(mms[, > x]), as.character(pns), as.integer(length(mms[, x])), > as.double(tau), as.double(sat), dpval = double(length(unique.pns)), > length(unique.pns), PACKAGE = "affy")$dpval > }) > 3: mas5calls.AffyBatch(object, ...) > 2: mas5calls(mydata) > 1: mas5calls(mydata) > > Kindly let me know if I am missing something, or whether it is possible that there is something wrong with the data. I tried using the "Dilution" dataset, and it seems to work. Thanks in advance. > > > Warm Regards > > Karthik Ramaswamy Padmanabhan > > M.S in Bioinformatics > Indiana University, Bloomington > > > > > [[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 > >

Hi Kartik, Karthik Ramaswamy Padmanabhan wrote: > Hello, > > I am trying to process some CEL files using the affy package in Bioconductor. I am using the steps given in the Bioconductor manual given here - http://manuals.bioinformatics.ucr.edu/home/R_BioCondManua l#biocon_affypack > > Here is the list of commands I used: > > mydata <- ReadAffy(cdfname = "hugene10stv1.r3cdf") >> eset <- rma(mydata) > Background correcting > Normalizing > Calculating Expression >> eset_PMA <- mas5calls(mydata) > Getting probe level data... > Computing p-values > Error in FUN(1:10[[1L]], ...) : > NA/NaN/Inf in foreign function call (arg 2) > > So, I am getting an error in the mas5calls function. Here is the sessionInfo(): And you should expect to. The HuGene chip is a PM-only chip, so trying to do MAS5 on it is not going to work. Best, Jim > > R version 2.10.1 (2009-12-14) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] hugene10stv1.r3cdf_2.5.0 affy_1.24.2 > [3] Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 preprocessCore_1.8.0 tools_2.10.1 > > And here is the traceback(): > > 7: .C("DetectionPValue", as.double(pms[, x]), as.double(mms[, x]), > as.character(pns), as.integer(length(mms[, x])), as.double(tau), > as.double(sat), dpval = double(length(unique.pns)), length(unique.pns), > PACKAGE = "affy") > 6: FUN(1:10[[1L]], ...) > 5: lapply(X, FUN, ...) > 4: sapply(1:length(pms[1, ]), function(x) { > .C("DetectionPValue", as.double(pms[, x]), as.double(mms[, > x]), as.character(pns), as.integer(length(mms[, x])), > as.double(tau), as.double(sat), dpval = double(length(unique.pns)), > length(unique.pns), PACKAGE = "affy")$dpval > }) > 3: mas5calls.AffyBatch(object, ...) > 2: mas5calls(mydata) > 1: mas5calls(mydata) > > Kindly let me know if I am missing something, or whether it is possible that there is something wrong with the data. I tried using the "Dilution" dataset, and it seems to work. Thanks in advance. > > > Warm Regards > > Karthik Ramaswamy Padmanabhan > > M.S in Bioinformatics > Indiana University, Bloomington > > > > > [[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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues