PVAC and Affymetrix HuGene array
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@tim-van-damme-5626
Last seen 6.8 years ago
Hello everyone I would like to use the pvac package to analyze data from Affymetrix HuGene 1.0 ST arrays. However, I keep getting this error when running the code: > raw <- ReadAffy(celfile.path="CELS") > library(pvac) > ft <- pvacFilter(raw) Making absent/present calls, preprocessing data ... Error in FUN(1:18[[1L]], ...) : NA/NaN/Inf in foreign function call (arg 2) > traceback() 8: .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") 7: FUN(1:18[[1L]], ...) 6: lapply(X = X, FUN = FUN, ...) 5: 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 }) 4: mas5calls.AffyBatch(object, ...) 3: mas5calls(abatch, verbose = FALSE) 2: mas5calls(abatch, verbose = FALSE) 1: pvacFilter(raw) > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] nl_BE.UTF-8/nl_BE.UTF-8/nl_BE.UTF-8/C/nl_BE.UTF-8/nl_BE.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] BiocInstaller_1.8.3 pvac_1.4.0 hgu133plus2cdf_2.10.0 [4] gplots_2.11.0 KernSmooth_2.23-8 caTools_1.13 [7] bitops_1.0-4.2 gdata_2.12.0 gtools_2.7.0 [10] RColorBrewer_1.0-5 statmod_1.4.16 limma_3.12.3 [13] farms_1.8.2 MASS_7.3-22 hugene10stv1cdf_2.10.0 [16] AnnotationDbi_1.18.4 affy_1.34.0 Biobase_2.16.0 [19] BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affyio_1.24.0 DBI_0.2-5 IRanges_1.14.4 [4] preprocessCore_1.18.0 RSQLite_0.11.2 stats4_2.15.1 [7] tools_2.15.1 zlibbioc_1.2.0 Any suggestions? Kind regards Tim [[alternative HTML version deleted]]
Preprocessing pvac Preprocessing pvac • 612 views
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@james-w-macdonald-5106
Last seen 10 hours ago
United States
Hi Tim, On 11/26/2012 10:56 AM, Tim Van Damme wrote: > Hello everyone > > I would like to use the pvac package to analyze data from Affymetrix HuGene 1.0 ST arrays. However, I keep getting this error when running the code: > >> raw<- ReadAffy(celfile.path="CELS") >> library(pvac) >> ft<- pvacFilter(raw) > Making absent/present calls, preprocessing data ... > Error in FUN(1:18[[1L]], ...) : > NA/NaN/Inf in foreign function call (arg 2) This is because the function is trying to compute present/absent calls, which are based on a comparison between the PM and MM probes. Since the HuGene array is a PM-only chip, this fails. You might contact the maintainer directly and see if they are planning to make a package that works with the newer Affy arrays. Best, Jim >> traceback() > 8: .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") > 7: FUN(1:18[[1L]], ...) > 6: lapply(X = X, FUN = FUN, ...) > 5: 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 > }) > 4: mas5calls.AffyBatch(object, ...) > 3: mas5calls(abatch, verbose = FALSE) > 2: mas5calls(abatch, verbose = FALSE) > 1: pvacFilter(raw) >> sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] nl_BE.UTF-8/nl_BE.UTF-8/nl_BE.UTF-8/C/nl_BE.UTF-8/nl_BE.UTF-8 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] BiocInstaller_1.8.3 pvac_1.4.0 hgu133plus2cdf_2.10.0 > [4] gplots_2.11.0 KernSmooth_2.23-8 caTools_1.13 > [7] bitops_1.0-4.2 gdata_2.12.0 gtools_2.7.0 > [10] RColorBrewer_1.0-5 statmod_1.4.16 limma_3.12.3 > [13] farms_1.8.2 MASS_7.3-22 hugene10stv1cdf_2.10.0 > [16] AnnotationDbi_1.18.4 affy_1.34.0 Biobase_2.16.0 > [19] BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] affyio_1.24.0 DBI_0.2-5 IRanges_1.14.4 > [4] preprocessCore_1.18.0 RSQLite_0.11.2 stats4_2.15.1 > [7] tools_2.15.1 zlibbioc_1.2.0 > > Any suggestions? > > Kind regards > Tim > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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 University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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