smoothing function in bumphunter in minfi
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@kasper-daniel-hansen-2979
Last seen 10 months ago
United States
I have been prompted on this off-list. Turns out I was reading the OP a bit too fast ... he is on R 3.0.3 which we no longer support (nor can I make changes to the relevant Bioconductor packages). So the solution is to upgrade to R-3.1. Hopefully that will fix the problem, otherwise get in touch. Whatever I have done would not have affected R 3.0.3. Best, Kasper On Wed, May 14, 2014 at 11:31 AM, Kasper Daniel Hansen <khansen@jhsph.edu> wrote: > This is a weirdly introduced error which we have fixed in the devel > branch. I was supposed to back port it into release, but I forgot. > > Kasper > > > On Wed, May 14, 2014 at 11:16 AM, Brad Ruzicka [guest] < > guest@bioconductor.org> wrote: > >> Hi there- >> I've been using bumphunter within minfi to analyze my HM450 dataset with >> good results, but I'm unable to use the smoothing function within >> bumphunter. When "smooth = TRUE" it gives the error: >> "Error in { : task 1 failed - "unused argument (cutoffQ = 0.99)"", even >> though I have not included cutoffQ in the script. >> >> The script below works fine with smooth = FALSE, but when set to true >> gives the above error: >> >> setwd("G:/Illumina/Brad/Minfi") >> baseDir <- "G:/Illumina/Brad/Minfi/Scan Output" >> targets <- read.450k.sheet(baseDir) >> RGSet <- read.450k.exp(base = baseDir, targets = targets) >> pd <- pData(RGSet) >> pd[,1:4] >> >> gRatioSet.quantile <- preprocessQuantile(RGSet, fixOutliers = TRUE, >> removeBadSamples = TRUE, badSampleCutoff = 10.5, quantileNormalize = TRUE, >> stratified = TRUE, mergeManifest = FALSE, sex = NULL) >> >> Age <- pData(gRatioSet.quantile)$age >> PMI <- pData(gRatioSet.quantile)$PMI >> diagnosis <- pData(gRatioSet.quantile)$diagnosis >> gender <- pData(gRatioSet.quantile)$gender >> >> designMatrix <- model.matrix(~ diagnosis + Age + PMI + gender) >> >> library(doParallel) >> registerDoParallel(cores = 4) >> dmrs <- bumphunter(gRatioSet.quantile, design = designMatrix, maxGap=500, >> pickCutoff = TRUE, smooth = TRUE, smoothFunction=locfitByCluster, B=1000) >> write.csv(dmrs$table, file = "GAD1BroadDMRsSZ3Test6.csv") >> >> Output of script: >> [read.450k.sheet] Found the following CSV files: >> [1] "G:/Illumina/Brad/Minfi/Scan Output/SampleSheetSZ32.csv" >> [preprocessQuantile] Mapping to genome. >> [preprocessQuantile] Fixing outliers. >> [preprocessQuantile] Quantile normalizing. >> [bumphunterEngine] Parallelizing using 4 workers/cores (backend: >> doParallelSNOW, version: 1.0.8). >> [bumphunterEngine] Computing coefficients. >> [bumphunterEngine] Smoothing coefficients. >> Error in { : task 1 failed - "unused argument (cutoffQ = 0.99)" >> >> Any ideas where my error is? >> Thanks, >> Brad >> >> -- output of sessionInfo(): >> >> > sessionInfo() >> R version 3.0.3 (2014-03-06) >> Platform: x86_64-w64-mingw32/x64 (64-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 >> [2] LC_CTYPE=English_United States.1252 >> [3] LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] doParallel_1.0.8 >> [2] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 >> [3] IlluminaHumanMethylation450kmanifest_0.4.0 >> [4] doRNG_1.6 >> [5] rngtools_1.2.4 >> [6] pkgmaker_0.20 >> [7] registry_0.2 >> [8] minfi_1.8.9 >> [9] bumphunter_1.2.0 >> [10] locfit_1.5-9.1 >> [11] iterators_1.0.7 >> [12] foreach_1.4.2 >> [13] Biostrings_2.30.1 >> [14] GenomicRanges_1.14.4 >> [15] XVector_0.2.0 >> [16] IRanges_1.20.7 >> [17] reshape_0.8.5 >> [18] lattice_0.20-29 >> [19] Biobase_2.22.0 >> [20] BiocGenerics_0.8.0 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.40.1 AnnotationDbi_1.24.0 base64_1.1 >> [4] beanplot_1.1 codetools_0.2-8 compiler_3.0.3 >> [7] DBI_0.2-7 digest_0.6.4 genefilter_1.44.0 >> [10] grid_3.0.3 illuminaio_0.4.0 itertools_0.1-3 >> [13] limma_3.18.13 MASS_7.3-33 matrixStats_0.8.14 >> [16] mclust_4.3 multtest_2.18.0 nlme_3.1-117 >> [19] nor1mix_1.1-4 plyr_1.8.1 preprocessCore_1.24.0 >> [22] R.methodsS3_1.6.1 RColorBrewer_1.0-5 Rcpp_0.11.1 >> [25] RSQLite_0.11.4 siggenes_1.36.0 splines_3.0.3 >> [28] stats4_3.0.3 stringr_0.6.2 survival_2.37-7 >> [31] tools_3.0.3 XML_3.98-1.1 xtable_1.7-3 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
minfi bumphunter minfi bumphunter • 1.5k views
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@ruzicka-william-bmd-6602
Last seen 7.7 years ago
Hi Kasper - Thanks for your help. I've upgraded to R-3.1.0 but bumphunter is still giving the same "unused aregument" error: > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] doParallel_1.0.8 IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 [3] IlluminaHumanMethylation450kmanifest_0.4.0 minfi_1.10.1 [5] bumphunter_1.4.2 locfit_1.5-9.1 [7] iterators_1.0.7 foreach_1.4.2 [9] Biostrings_2.32.0 XVector_0.4.0 [11] GenomicRanges_1.16.3 GenomeInfoDb_1.0.2 [13] IRanges_1.22.8 lattice_0.20-29 [15] Biobase_2.24.0 BiocGenerics_0.10.0 loaded via a namespace (and not attached): [1] annotate_1.42.0 AnnotationDbi_1.26.0 base64_1.1 beanplot_1.1 [5] codetools_0.2-8 compiler_3.1.0 DBI_0.2-7 digest_0.6.4 [9] doRNG_1.6 genefilter_1.46.1 grid_3.1.0 illuminaio_0.6.0 [13] limma_3.20.4 MASS_7.3-33 matrixStats_0.10.0 mclust_4.3 [17] multtest_2.20.0 nlme_3.1-117 nor1mix_1.1-4 pkgmaker_0.22 [21] plyr_1.8.1 preprocessCore_1.26.1 R.methodsS3_1.6.1 RColorBrewer_1.0-5 [25] Rcpp_0.11.2 registry_0.2 reshape_0.8.5 rngtools_1.2.4 [29] RSQLite_0.11.4 siggenes_1.38.0 splines_3.1.0 stats4_3.1.0 [33] stringr_0.6.2 survival_2.37-7 tools_3.1.0 XML_3.98-1.1 [37] xtable_1.7-3 zlibbioc_1.10.0 > traceback() 10: stop(simpleError(msg, call = expr)) 9: e$fun(obj, substitute(ex), parent.frame(), e$data) 8: list(args = iter(IndexesChunks)(.doRNG.stream = list(c(407L, -631507724L, 2080869221L, 1065599202L, 1311698683L, -323805696L, -1040906751L), c(407L, 1945611946L, -608207003L, 1842430237L, -518903442L, 1824620966L, -1548636643L), c(407L, 237898474L, 1062912735L, -1334786133L, 1059436525L, 793963592L, 1493198629L ), c(407L, 1527452477L, -1461135650L, 1252537885L, 1975038170L, -892552789L, -512077693L))), argnames = c("idx", ".doRNG.stream" ), evalenv = <environment>, specified = character(0), combineInfo = list( fun = function (a, ...) c(a, list(...)), in.order = TRUE, has.init = TRUE, init = list(), final = NULL, multi.combine = TRUE, max.combine = 100), errorHandling = "stop", packages = c("bumphunter", "doRNG"), export = NULL, noexport = NULL, options = list(), verbose = FALSE) %dopar% { { rngtools::RNGseed(.doRNG.stream) } { sm <- smoothFunction(y = y[idx, ], x = x[idx], cluster = cluster[idx], weights = weights[idx, ], verbose = verbose, ...) c(sm, list(idx = idx)) } } 7: do.call("%dopar%", list(obj, ex), envir = parent.frame()) 6: foreach(idx = iter(IndexesChunks), .packages = "bumphunter") %dorng% { sm <- smoothFunction(y = y[idx, ], x = x[idx], cluster = cluster[idx], weights = weights[idx, ], verbose = verbose, ...) c(sm, list(idx = idx)) } 5: smoother(y = rawBeta, x = pos, cluster = cluster, weights = weights, smoothFunction = smoothFunction, verbose = subverbose, ...) 4: bumphunterEngine(getMethSignal(object, type), design = design, chr = as.factor(seqnames(object)), pos = start(object), cluster = cluster, coef = coef, cutoff = cutoff, cutoffQ = cutoffQ, maxGap = maxGap, smooth = smooth, smoothFunction = smoothFunction, useWeights = useWeights, B = B, verbose = verbose, ...) 3: .local(object, ...) 2: bumphunter(GRQ, design = designMatrix, pickCutoff = TRUE, B = 100, maxGap = 500, smooth = TRUE, smoothFunction = locfitByCluster) 1: bumphunter(GRQ, design = designMatrix, pickCutoff = TRUE, B = 100, maxGap = 500, smooth = TRUE, smoothFunction = locfitByCluster) R version 3.1.0 (2014-04-10) -- "Spring Dance" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. [Workspace loaded from ~/.RData] > require(minfi) Loading required package: minfi Loading required package: BiocGenerics Loading required package: parallel Attaching package: ?BiocGenerics? The following objects are masked from ?package:parallel? clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ?package:stats? xtabs The following objects are masked from ?package:base? anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: lattice Loading required package: GenomicRanges Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Biostrings Loading required package: XVector Loading required package: bumphunter Loading required package: foreach foreach: simple, scalable parallel programming from Revolution Analytics Use Revolution R for scalability, fault tolerance and more. http://www.revolutionanalytics.com Loading required package: iterators Loading required package: locfit locfit 1.5-9.1 2013-03-22 > setwd("G:/Illumina/Brad/Minfi") > baseDir <- "G:/Illumina/Brad/Minfi/Scan Output" > targets <- read.450k.sheet(baseDir) [read.450k.sheet] Found the following CSV files: [1] "G:/Illumina/Brad/Minfi/Scan Output/SampleSheetSZ32.csv" > RGSet <- read.450k.exp(base = baseDir, targets = targets) > pd <- pData(RGSet) > pd[,1:4] Sample_Name Sample_Well Sample_Plate Sample_Group 8942300007_R02C01 CON1_CA32 B01 Plate1 CON_CA32 8942300010_R06C01 CON2_CA32 B01 Plate1 CON_CA32 8942297078_R06C01 CON3_CA32 F02 Plate1 CON_CA32 8942300010_R01C01 CON4_CA32 E02 Plate1 CON_CA32 8942300010_R05C01 CON5_CA32 A01 Plate1 CON_CA32 8942297143_R06C02 CON6_CA32 H02 Plate1 CON_CA32 8942297143_R06C01 CON7_CA32 B02 Plate1 CON_CA32 8942297143_R01C02 CON8_CA32 C02 Plate1 CON_CA32 8942300007_R01C01 SZ1_CA32 A01 Plate1 SZ_CA32 8942300007_R03C01 SZ2_CA32 C01 Plate1 SZ_CA32 8942297078_R03C02 SZ3_CA32 A01 Plate1 SZ_CA32 8942300010_R02C01 SZ4_CA32 F02 Plate1 SZ_CA32 8942300010_R02C02 SZ5_CA32 D01 Plate1 SZ_CA32 8942297078_R01C01 SZ6_CA32 A02 Plate1 SZ_CA32 8942297143_R04C01 SZ7_CA32 H01 Plate1 SZ_CA32 8942297078_R06C02 SZ8_CA32 D01 Plate1 SZ_CA32 > > gRatioSet.quantile <- preprocessQuantile(RGSet, fixOutliers = TRUE, removeBadSamples = TRUE, badSampleCutoff = 10.5, quantileNormalize = TRUE, stratified = TRUE, mergeManifest = FALSE, sex = NULL) [preprocessQuantile] Mapping to genome. Loading required package: IlluminaHumanMethylation450kmanifest Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19 [preprocessQuantile] Fixing outliers. [preprocessQuantile] Quantile normalizing. > > GADBroad <- read.csv("GAD1LessBroad.csv") > GRSGADBroad <- as.vector(GADBroad) > Test <- GADBroad[1:1856,1] > MSetGADBroad <- as.vector(GADBroad[,1]) > GRQ <- gRatioSet.quantile[Test] > diagnosis <- pData(gRatioSet.quantile)$diagnosis > designMatrix <- model.matrix(~ diagnosis) > library(doParallel) > registerDoParallel(cores = 4) > dmrs <- bumphunter(GRQ, design = designMatrix, pickCutoff = TRUE, B=100, maxGap=500, smooth=TRUE, smoothFunction=locfitByCluster) [bumphunterEngine] Parallelizing using 4 workers/cores (backend: doParallelSNOW, version: 1.0.8). [bumphunterEngine] Computing coefficients. [bumphunterEngine] Smoothing coefficients. Error in { : task 1 failed - "unused argument (cutoffQ = 0.99)" - Brad ________________________________ From: kasperdanielhansen@gmail.com [kasperdanielhansen@gmail.com] on behalf of Kasper Daniel Hansen [khansen@jhsph.edu] Sent: Tuesday, June 10, 2014 9:48 PM To: Brad Ruzicka [guest] Cc: bioconductor at r-project.org; Ruzicka, William B.,M.D. Subject: Re: [BioC] smoothing function in bumphunter in minfi I have been prompted on this off-list. Turns out I was reading the OP a bit too fast ... he is on R 3.0.3 which we no longer support (nor can I make changes to the relevant Bioconductor packages). So the solution is to upgrade to R-3.1. Hopefully that will fix the problem, otherwise get in touch. Whatever I have done would not have affected R 3.0.3. Best, Kasper On Wed, May 14, 2014 at 11:31 AM, Kasper Daniel Hansen <khansen at="" jhsph.edu<mailto:khansen="" at="" jhsph.edu="">> wrote: This is a weirdly introduced error which we have fixed in the devel branch. I was supposed to back port it into release, but I forgot. Kasper On Wed, May 14, 2014 at 11:16 AM, Brad Ruzicka [guest] <guest at="" bioconductor.org<mailto:guest="" at="" bioconductor.org="">> wrote: Hi there- I've been using bumphunter within minfi to analyze my HM450 dataset with good results, but I'm unable to use the smoothing function within bumphunter. When "smooth = TRUE" it gives the error: "Error in { : task 1 failed - "unused argument (cutoffQ = 0.99)"", even though I have not included cutoffQ in the script. The script below works fine with smooth = FALSE, but when set to true gives the above error: setwd("G:/Illumina/Brad/Minfi") baseDir <- "G:/Illumina/Brad/Minfi/Scan Output" targets <- read.450k.sheet(baseDir) RGSet <- read.450k.exp(base = baseDir, targets = targets) pd <- pData(RGSet) pd[,1:4] gRatioSet.quantile <- preprocessQuantile(RGSet, fixOutliers = TRUE, removeBadSamples = TRUE, badSampleCutoff = 10.5, quantileNormalize = TRUE, stratified = TRUE, mergeManifest = FALSE, sex = NULL) Age <- pData(gRatioSet.quantile)$age PMI <- pData(gRatioSet.quantile)$PMI diagnosis <- pData(gRatioSet.quantile)$diagnosis gender <- pData(gRatioSet.quantile)$gender designMatrix <- model.matrix(~ diagnosis + Age + PMI + gender) library(doParallel) registerDoParallel(cores = 4) dmrs <- bumphunter(gRatioSet.quantile, design = designMatrix, maxGap=500, pickCutoff = TRUE, smooth = TRUE, smoothFunction=locfitByCluster, B=1000) write.csv(dmrs$table, file = "GAD1BroadDMRsSZ3Test6.csv") Output of script: [read.450k.sheet] Found the following CSV files: [1] "G:/Illumina/Brad/Minfi/Scan Output/SampleSheetSZ32.csv" [preprocessQuantile] Mapping to genome. [preprocessQuantile] Fixing outliers. [preprocessQuantile] Quantile normalizing. [bumphunterEngine] Parallelizing using 4 workers/cores (backend: doParallelSNOW, version: 1.0.8). [bumphunterEngine] Computing coefficients. [bumphunterEngine] Smoothing coefficients. Error in { : task 1 failed - "unused argument (cutoffQ = 0.99)" Any ideas where my error is? Thanks, Brad -- output of sessionInfo(): > sessionInfo() R version 3.0.3 (2014-03-06) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] doParallel_1.0.8 [2] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 [3] IlluminaHumanMethylation450kmanifest_0.4.0 [4] doRNG_1.6 [5] rngtools_1.2.4 [6] pkgmaker_0.20 [7] registry_0.2 [8] minfi_1.8.9 [9] bumphunter_1.2.0 [10] locfit_1.5-9.1 [11] iterators_1.0.7 [12] foreach_1.4.2 [13] Biostrings_2.30.1 [14] GenomicRanges_1.14.4 [15] XVector_0.2.0 [16] IRanges_1.20.7 [17] reshape_0.8.5 [18] lattice_0.20-29 [19] Biobase_2.22.0 [20] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] annotate_1.40.1 AnnotationDbi_1.24.0 base64_1.1 [4] beanplot_1.1 codetools_0.2-8 compiler_3.0.3 [7] DBI_0.2-7 digest_0.6.4 genefilter_1.44.0 [10] grid_3.0.3 illuminaio_0.4.0 itertools_0.1-3 [13] limma_3.18.13 MASS_7.3-33 matrixStats_0.8.14 [16] mclust_4.3 multtest_2.18.0 nlme_3.1-117 [19] nor1mix_1.1-4 plyr_1.8.1 preprocessCore_1.24.0 [22] R.methodsS3_1.6.1 RColorBrewer_1.0-5 Rcpp_0.11.1 [25] RSQLite_0.11.4 siggenes_1.36.0 splines_3.0.3 [28] stats4_3.0.3 stringr_0.6.2 survival_2.37-7 [31] tools_3.0.3 XML_3.98-1.1 xtable_1.7-3 -- Sent via the guest posting facility at bioconductor.org<http: bioconductor.org="">. _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -------------- next part -------------- The information in this e-mail is intended only for the person to whom it is addressed. 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@kasper-daniel-hansen-2979
Last seen 10 months ago
United States
Ok Brad, after your cry for help on another forum I have spent some more time and I are now able to reproduce your problem (the fact I could not reproduce it earlier, was entirely my fault I now realize). I will try to submit a fix tonight, and will report back here when it is done. Sorry for the trouble. Best, Kasper On Wed, Jun 11, 2014 at 10:50 AM, Ruzicka, William B.,M.D. < wruzicka@mclean.harvard.edu> wrote: > Hi Kasper - > Thanks for your help. > I've upgraded to R-3.1.0 but bumphunter is still giving the same "unused > aregument" error: > > > > > sessionInfo() > > R version 3.1.0 (2014-04-10) > > Platform: x86_64-w64-mingw32/x64 (64-bit) > > > > locale: > > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 > > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > > > [5] LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] parallel stats graphics grDevices utils datasets methods > base > > > > other attached packages: > > [1] doParallel_1.0.8 > IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 > > [3] IlluminaHumanMethylation450kmanifest_0.4.0 minfi_1.10.1 > > > [5] bumphunter_1.4.2 locfit_1.5-9.1 > > > [7] iterators_1.0.7 foreach_1.4.2 > > > [9] Biostrings_2.32.0 XVector_0.4.0 > > > [11] GenomicRanges_1.16.3 GenomeInfoDb_1.0.2 > > > [13] IRanges_1.22.8 lattice_0.20-29 > > > [15] Biobase_2.24.0 > BiocGenerics_0.10.0 > > > > loaded via a namespace (and not attached): > > [1] annotate_1.42.0 AnnotationDbi_1.26.0 base64_1.1 > beanplot_1.1 > > [5] codetools_0.2-8 compiler_3.1.0 DBI_0.2-7 > digest_0.6.4 > > [9] doRNG_1.6 genefilter_1.46.1 grid_3.1.0 > illuminaio_0.6.0 > > [13] limma_3.20.4 MASS_7.3-33 matrixStats_0.10.0 > mclust_4.3 > > [17] multtest_2.20.0 nlme_3.1-117 nor1mix_1.1-4 > pkgmaker_0.22 > > [21] plyr_1.8.1 preprocessCore_1.26.1 R.methodsS3_1.6.1 > RColorBrewer_1.0-5 > > [25] Rcpp_0.11.2 registry_0.2 reshape_0.8.5 > rngtools_1.2.4 > > [29] RSQLite_0.11.4 siggenes_1.38.0 splines_3.1.0 > stats4_3.1.0 > > [33] stringr_0.6.2 survival_2.37-7 tools_3.1.0 > XML_3.98-1.1 > > [37] xtable_1.7-3 zlibbioc_1.10.0 > > > > > traceback() > > 10: stop(simpleError(msg, call = expr)) > > 9: e$fun(obj, substitute(ex), parent.frame(), e$data) > > 8: list(args = iter(IndexesChunks)(.doRNG.stream = list(c(407L, > > -631507724L, 2080869221L, 1065599202L, 1311698683L, -323805696L, > > -1040906751L), c(407L, 1945611946L, -608207003L, 1842430237L, > > -518903442L, 1824620966L, -1548636643L), c(407L, 237898474L, > > 1062912735L, -1334786133L, 1059436525L, 793963592L, 1493198629L > > ), c(407L, 1527452477L, -1461135650L, 1252537885L, 1975038170L, > > -892552789L, -512077693L))), argnames = c("idx", ".doRNG.stream" > > ), evalenv = <environment>, specified = character(0), combineInfo = list( > > fun = function (a, ...) > > c(a, list(...)), in.order = TRUE, has.init = TRUE, init = list(), > > final = NULL, multi.combine = TRUE, max.combine = 100), errorHandling = "stop", > > packages = c("bumphunter", "doRNG"), export = NULL, noexport = NULL, > > options = list(), verbose = FALSE) %dopar% { > > { > > rngtools::RNGseed(.doRNG.stream) > > } > > { > > sm <- smoothFunction(y = y[idx, ], x = x[idx], cluster = cluster[idx], > > weights = weights[idx, ], verbose = verbose, ...) > > c(sm, list(idx = idx)) > > } > > } > > 7: do.call("%dopar%", list(obj, ex), envir = parent.frame()) > > 6: foreach(idx = iter(IndexesChunks), .packages = "bumphunter") %dorng% > > { > > sm <- smoothFunction(y = y[idx, ], x = x[idx], cluster = cluster[idx], > > weights = weights[idx, ], verbose = verbose, ...) > > c(sm, list(idx = idx)) > > } > > 5: smoother(y = rawBeta, x = pos, cluster = cluster, weights = weights, > > smoothFunction = smoothFunction, verbose = subverbose, ...) > > 4: bumphunterEngine(getMethSignal(object, type), design = design, > > chr = as.factor(seqnames(object)), pos = start(object), cluster = cluster, > > coef = coef, cutoff = cutoff, cutoffQ = cutoffQ, maxGap = maxGap, > > smooth = smooth, smoothFunction = smoothFunction, useWeights = useWeights, > > B = B, verbose = verbose, ...) > > 3: .local(object, ...) > > 2: bumphunter(GRQ, design = designMatrix, pickCutoff = TRUE, B = 100, > > maxGap = 500, smooth = TRUE, smoothFunction = locfitByCluster) > > 1: bumphunter(GRQ, design = designMatrix, pickCutoff = TRUE, B = 100, > > maxGap = 500, smooth = TRUE, smoothFunction = locfitByCluster) > > > > R version 3.1.0 (2014-04-10) -- "Spring Dance" > > Copyright (C) 2014 The R Foundation for Statistical Computing > > Platform: x86_64-w64-mingw32/x64 (64-bit) > > > > R is free software and comes with ABSOLUTELY NO WARRANTY. > > You are welcome to redistribute it under certain conditions. > > Type 'license()' or 'licence()' for distribution details. > > > > R is a collaborative project with many contributors. > > Type 'contributors()' for more information and > > 'citation()' on how to cite R or R packages in publications. > > > > Type 'demo()' for some demos, 'help()' for on-line help, or > > 'help.start()' for an HTML browser interface to help. > > Type 'q()' to quit R. > > > > [Workspace loaded from ~/.RData] > > > > > require(minfi) > > Loading required package: minfi > > Loading required package: BiocGenerics > > Loading required package: parallel > > > > Attaching package: æ ‹iocGenerics? > > The following objects are masked from 憄ackage:parallel? > > > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, > > parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB > > > > The following object is masked from 憄ackage:stats? > > > > xtabs > > > > The following objects are masked from 憄ackage:base? > > > > anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, > > evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, > > paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, > > sapply, setdiff, sort, table, tapply, union, unique, unlist > > > > Loading required package: Biobase > > Welcome to Bioconductor > > > > Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, > > see 'citation("Biobase")', and for packages 'citation("pkgname")'. > > > > Loading required package: lattice > > Loading required package: GenomicRanges > > Loading required package: IRanges > > Loading required package: GenomeInfoDb > > Loading required package: Biostrings > > Loading required package: XVector > > Loading required package: bumphunter > > Loading required package: foreach > > foreach: simple, scalable parallel programming from Revolution Analytics > > Use Revolution R for scalability, fault tolerance and more. > > http://www.revolutionanalytics.com > > Loading required package: iterators > > Loading required package: locfit > > locfit 1.5-9.1 2013-03-22 > > > setwd("G:/Illumina/Brad/Minfi") > > > baseDir <- "G:/Illumina/Brad/Minfi/Scan Output" > > > targets <- read.450k.sheet(baseDir) > > [read.450k.sheet] Found the following CSV files: > > [1] "G:/Illumina/Brad/Minfi/Scan Output/SampleSheetSZ32.csv" > > > RGSet <- read.450k.exp(base = baseDir, targets = targets) > > > pd <- pData(RGSet) > > > pd[,1:4] > > Sample_Name Sample_Well Sample_Plate Sample_Group > > 8942300007_R02C01 CON1_CA32 B01 Plate1 CON_CA32 > > 8942300010_R06C01 CON2_CA32 B01 Plate1 CON_CA32 > > 8942297078_R06C01 CON3_CA32 F02 Plate1 CON_CA32 > > 8942300010_R01C01 CON4_CA32 E02 Plate1 CON_CA32 > > 8942300010_R05C01 CON5_CA32 A01 Plate1 CON_CA32 > > 8942297143_R06C02 CON6_CA32 H02 Plate1 CON_CA32 > > 8942297143_R06C01 CON7_CA32 B02 Plate1 CON_CA32 > > 8942297143_R01C02 CON8_CA32 C02 Plate1 CON_CA32 > > 8942300007_R01C01 SZ1_CA32 A01 Plate1 SZ_CA32 > > 8942300007_R03C01 SZ2_CA32 C01 Plate1 SZ_CA32 > > 8942297078_R03C02 SZ3_CA32 A01 Plate1 SZ_CA32 > > 8942300010_R02C01 SZ4_CA32 F02 Plate1 SZ_CA32 > > 8942300010_R02C02 SZ5_CA32 D01 Plate1 SZ_CA32 > > 8942297078_R01C01 SZ6_CA32 A02 Plate1 SZ_CA32 > > 8942297143_R04C01 SZ7_CA32 H01 Plate1 SZ_CA32 > > 8942297078_R06C02 SZ8_CA32 D01 Plate1 SZ_CA32 > > > > > > gRatioSet.quantile <- preprocessQuantile(RGSet, fixOutliers = TRUE, removeBadSamples = TRUE, badSampleCutoff = 10.5, quantileNormalize = TRUE, stratified = TRUE, mergeManifest = FALSE, sex = NULL) > > [preprocessQuantile] Mapping to genome. > > Loading required package: IlluminaHumanMethylation450kmanifest > > Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19 > > [preprocessQuantile] Fixing outliers. > > [preprocessQuantile] Quantile normalizing. > > > > > > GADBroad <- read.csv("GAD1LessBroad.csv") > > > GRSGADBroad <- as.vector(GADBroad) > > > Test <- GADBroad[1:1856,1] > > > MSetGADBroad <- as.vector(GADBroad[,1]) > > > GRQ <- gRatioSet.quantile[Test] > > > diagnosis <- pData(gRatioSet.quantile)$diagnosis > > > designMatrix <- model.matrix(~ diagnosis) > > > library(doParallel) > > > registerDoParallel(cores = 4) > > > dmrs <- bumphunter(GRQ, design = designMatrix, pickCutoff = TRUE, B=100, maxGap=500, smooth=TRUE, smoothFunction=locfitByCluster) > > [bumphunterEngine] Parallelizing using 4 workers/cores (backend: doParallelSNOW, version: 1.0.8). > > [bumphunterEngine] Computing coefficients. > > [bumphunterEngine] Smoothing coefficients. > > Error in { : task 1 failed - "unused argument (cutoffQ = 0.99)" > > > - Brad > > ------------------------------ > *From:* kasperdanielhansen@gmail.com [kasperdanielhansen@gmail.com] on > behalf of Kasper Daniel Hansen [khansen@jhsph.edu] > *Sent:* Tuesday, June 10, 2014 9:48 PM > *To:* Brad Ruzicka [guest] > *Cc:* bioconductor@r-project.org; Ruzicka, William B.,M.D. > *Subject:* Re: [BioC] smoothing function in bumphunter in minfi > > I have been prompted on this off-list. Turns out I was reading the OP > a bit too fast ... he is on R 3.0.3 which we no longer support (nor can I > make changes to the relevant Bioconductor packages). So the solution is to > upgrade to R-3.1. > > Hopefully that will fix the problem, otherwise get in touch. Whatever I > have done would not have affected R 3.0.3. > > Best, > Kasper > > > On Wed, May 14, 2014 at 11:31 AM, Kasper Daniel Hansen <khansen@jhsph.edu> > wrote: > >> This is a weirdly introduced error which we have fixed in the devel >> branch. I was supposed to back port it into release, but I forgot. >> >> Kasper >> >> >> On Wed, May 14, 2014 at 11:16 AM, Brad Ruzicka [guest] < >> guest@bioconductor.org> wrote: >> >>> Hi there- >>> I've been using bumphunter within minfi to analyze my HM450 dataset with >>> good results, but I'm unable to use the smoothing function within >>> bumphunter. When "smooth = TRUE" it gives the error: >>> "Error in { : task 1 failed - "unused argument (cutoffQ = 0.99)"", even >>> though I have not included cutoffQ in the script. >>> >>> The script below works fine with smooth = FALSE, but when set to true >>> gives the above error: >>> >>> setwd("G:/Illumina/Brad/Minfi") >>> baseDir <- "G:/Illumina/Brad/Minfi/Scan Output" >>> targets <- read.450k.sheet(baseDir) >>> RGSet <- read.450k.exp(base = baseDir, targets = targets) >>> pd <- pData(RGSet) >>> pd[,1:4] >>> >>> gRatioSet.quantile <- preprocessQuantile(RGSet, fixOutliers = TRUE, >>> removeBadSamples = TRUE, badSampleCutoff = 10.5, quantileNormalize = TRUE, >>> stratified = TRUE, mergeManifest = FALSE, sex = NULL) >>> >>> Age <- pData(gRatioSet.quantile)$age >>> PMI <- pData(gRatioSet.quantile)$PMI >>> diagnosis <- pData(gRatioSet.quantile)$diagnosis >>> gender <- pData(gRatioSet.quantile)$gender >>> >>> designMatrix <- model.matrix(~ diagnosis + Age + PMI + gender) >>> >>> library(doParallel) >>> registerDoParallel(cores = 4) >>> dmrs <- bumphunter(gRatioSet.quantile, design = designMatrix, >>> maxGap=500, pickCutoff = TRUE, smooth = TRUE, >>> smoothFunction=locfitByCluster, B=1000) >>> write.csv(dmrs$table, file = "GAD1BroadDMRsSZ3Test6.csv") >>> >>> Output of script: >>> [read.450k.sheet] Found the following CSV files: >>> [1] "G:/Illumina/Brad/Minfi/Scan Output/SampleSheetSZ32.csv" >>> [preprocessQuantile] Mapping to genome. >>> [preprocessQuantile] Fixing outliers. >>> [preprocessQuantile] Quantile normalizing. >>> [bumphunterEngine] Parallelizing using 4 workers/cores (backend: >>> doParallelSNOW, version: 1.0.8). >>> [bumphunterEngine] Computing coefficients. >>> [bumphunterEngine] Smoothing coefficients. >>> Error in { : task 1 failed - "unused argument (cutoffQ = 0.99)" >>> >>> Any ideas where my error is? >>> Thanks, >>> Brad >>> >>> -- output of sessionInfo(): >>> >>> > sessionInfo() >>> R version 3.0.3 (2014-03-06) >>> Platform: x86_64-w64-mingw32/x64 (64-bit) >>> >>> locale: >>> [1] LC_COLLATE=English_United States.1252 >>> [2] LC_CTYPE=English_United States.1252 >>> [3] LC_MONETARY=English_United States.1252 >>> [4] LC_NUMERIC=C >>> [5] LC_TIME=English_United States.1252 >>> >>> attached base packages: >>> [1] parallel stats graphics grDevices utils datasets methods >>> [8] base >>> >>> other attached packages: >>> [1] doParallel_1.0.8 >>> [2] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 >>> [3] IlluminaHumanMethylation450kmanifest_0.4.0 >>> [4] doRNG_1.6 >>> [5] rngtools_1.2.4 >>> [6] pkgmaker_0.20 >>> [7] registry_0.2 >>> [8] minfi_1.8.9 >>> [9] bumphunter_1.2.0 >>> [10] locfit_1.5-9.1 >>> [11] iterators_1.0.7 >>> [12] foreach_1.4.2 >>> [13] Biostrings_2.30.1 >>> [14] GenomicRanges_1.14.4 >>> [15] XVector_0.2.0 >>> [16] IRanges_1.20.7 >>> [17] reshape_0.8.5 >>> [18] lattice_0.20-29 >>> [19] Biobase_2.22.0 >>> [20] BiocGenerics_0.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] annotate_1.40.1 AnnotationDbi_1.24.0 base64_1.1 >>> [4] beanplot_1.1 codetools_0.2-8 compiler_3.0.3 >>> [7] DBI_0.2-7 digest_0.6.4 genefilter_1.44.0 >>> [10] grid_3.0.3 illuminaio_0.4.0 itertools_0.1-3 >>> [13] limma_3.18.13 MASS_7.3-33 matrixStats_0.8.14 >>> [16] mclust_4.3 multtest_2.18.0 nlme_3.1-117 >>> [19] nor1mix_1.1-4 plyr_1.8.1 preprocessCore_1.24.0 >>> [22] R.methodsS3_1.6.1 RColorBrewer_1.0-5 Rcpp_0.11.1 >>> [25] RSQLite_0.11.4 siggenes_1.36.0 splines_3.0.3 >>> [28] stats4_3.0.3 stringr_0.6.2 survival_2.37-7 >>> [31] tools_3.0.3 XML_3.98-1.1 xtable_1.7-3 >>> >>> -- >>> Sent via the guest posting facility at bioconductor.org. >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > [[alternative HTML version deleted]]
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Just committed minfi 1.10.2 which should fix this issue. I hope... Best, Kasper On Fri, Jun 13, 2014 at 2:50 PM, Kasper Daniel Hansen <khansen@jhsph.edu> wrote: > Ok Brad, after your cry for help on another forum I have spent some more > time and I are now able to reproduce your problem (the fact I could not > reproduce it earlier, was entirely my fault I now realize). I will try to > submit a fix tonight, and will report back here when it is done. Sorry for > the trouble. > > Best, > Kasper > > > On Wed, Jun 11, 2014 at 10:50 AM, Ruzicka, William B.,M.D. < > wruzicka@mclean.harvard.edu> wrote: > >> Hi Kasper - >> Thanks for your help. >> I've upgraded to R-3.1.0 but bumphunter is still giving the same "unused >> aregument" error: >> >> >> >> > sessionInfo() >> >> R version 3.1.0 (2014-04-10) >> >> Platform: x86_64-w64-mingw32/x64 (64-bit) >> >> >> >> locale: >> >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> States.1252 >> >> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C >> >> >> [5] LC_TIME=English_United States.1252 >> >> >> >> attached base packages: >> >> [1] parallel stats graphics grDevices utils datasets methods >> base >> >> >> >> other attached packages: >> >> [1] doParallel_1.0.8 >> IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 >> >> [3] IlluminaHumanMethylation450kmanifest_0.4.0 minfi_1.10.1 >> >> >> [5] bumphunter_1.4.2 locfit_1.5-9.1 >> >> >> [7] iterators_1.0.7 foreach_1.4.2 >> >> >> [9] Biostrings_2.32.0 XVector_0.4.0 >> >> >> [11] GenomicRanges_1.16.3 >> GenomeInfoDb_1.0.2 >> >> [13] IRanges_1.22.8 lattice_0.20-29 >> >> >> [15] Biobase_2.24.0 >> BiocGenerics_0.10.0 >> >> >> >> loaded via a namespace (and not attached): >> >> [1] annotate_1.42.0 AnnotationDbi_1.26.0 base64_1.1 >> beanplot_1.1 >> >> [5] codetools_0.2-8 compiler_3.1.0 DBI_0.2-7 >> digest_0.6.4 >> >> [9] doRNG_1.6 genefilter_1.46.1 grid_3.1.0 >> illuminaio_0.6.0 >> >> [13] limma_3.20.4 MASS_7.3-33 matrixStats_0.10.0 >> mclust_4.3 >> >> [17] multtest_2.20.0 nlme_3.1-117 nor1mix_1.1-4 >> pkgmaker_0.22 >> >> [21] plyr_1.8.1 preprocessCore_1.26.1 R.methodsS3_1.6.1 >> RColorBrewer_1.0-5 >> >> [25] Rcpp_0.11.2 registry_0.2 reshape_0.8.5 >> rngtools_1.2.4 >> >> [29] RSQLite_0.11.4 siggenes_1.38.0 splines_3.1.0 >> stats4_3.1.0 >> >> [33] stringr_0.6.2 survival_2.37-7 tools_3.1.0 >> XML_3.98-1.1 >> >> [37] xtable_1.7-3 zlibbioc_1.10.0 >> >> >> >> > traceback() >> >> 10: stop(simpleError(msg, call = expr)) >> >> 9: e$fun(obj, substitute(ex), parent.frame(), e$data) >> >> 8: list(args = iter(IndexesChunks)(.doRNG.stream = list(c(407L, >> >> -631507724L, 2080869221L, 1065599202L, 1311698683L, -323805696L, >> >> -1040906751L), c(407L, 1945611946L, -608207003L, 1842430237L, >> >> -518903442L, 1824620966L, -1548636643L), c(407L, 237898474L, >> >> 1062912735L, -1334786133L, 1059436525L, 793963592L, 1493198629L >> >> ), c(407L, 1527452477L, -1461135650L, 1252537885L, 1975038170L, >> >> -892552789L, -512077693L))), argnames = c("idx", ".doRNG.stream" >> >> ), evalenv = <environment>, specified = character(0), combineInfo = list( >> >> fun = function (a, ...) >> >> c(a, list(...)), in.order = TRUE, has.init = TRUE, init = list(), >> >> final = NULL, multi.combine = TRUE, max.combine = 100), errorHandling = "stop", >> >> packages = c("bumphunter", "doRNG"), export = NULL, noexport = NULL, >> >> options = list(), verbose = FALSE) %dopar% { >> >> { >> >> rngtools::RNGseed(.doRNG.stream) >> >> } >> >> { >> >> sm <- smoothFunction(y = y[idx, ], x = x[idx], cluster = cluster[idx], >> >> weights = weights[idx, ], verbose = verbose, ...) >> >> c(sm, list(idx = idx)) >> >> } >> >> } >> >> 7: do.call("%dopar%", list(obj, ex), envir = parent.frame()) >> >> 6: foreach(idx = iter(IndexesChunks), .packages = "bumphunter") %dorng% >> >> { >> >> sm <- smoothFunction(y = y[idx, ], x = x[idx], cluster = cluster[idx], >> >> weights = weights[idx, ], verbose = verbose, ...) >> >> c(sm, list(idx = idx)) >> >> } >> >> 5: smoother(y = rawBeta, x = pos, cluster = cluster, weights = weights, >> >> smoothFunction = smoothFunction, verbose = subverbose, ...) >> >> 4: bumphunterEngine(getMethSignal(object, type), design = design, >> >> chr = as.factor(seqnames(object)), pos = start(object), cluster = cluster, >> >> coef = coef, cutoff = cutoff, cutoffQ = cutoffQ, maxGap = maxGap, >> >> smooth = smooth, smoothFunction = smoothFunction, useWeights = useWeights, >> >> B = B, verbose = verbose, ...) >> >> 3: .local(object, ...) >> >> 2: bumphunter(GRQ, design = designMatrix, pickCutoff = TRUE, B = 100, >> >> maxGap = 500, smooth = TRUE, smoothFunction = locfitByCluster) >> >> 1: bumphunter(GRQ, design = designMatrix, pickCutoff = TRUE, B = 100, >> >> maxGap = 500, smooth = TRUE, smoothFunction = locfitByCluster) >> >> >> >> R version 3.1.0 (2014-04-10) -- "Spring Dance" >> >> Copyright (C) 2014 The R Foundation for Statistical Computing >> >> Platform: x86_64-w64-mingw32/x64 (64-bit) >> >> >> >> R is free software and comes with ABSOLUTELY NO WARRANTY. >> >> You are welcome to redistribute it under certain conditions. >> >> Type 'license()' or 'licence()' for distribution details. >> >> >> >> R is a collaborative project with many contributors. >> >> Type 'contributors()' for more information and >> >> 'citation()' on how to cite R or R packages in publications. >> >> >> >> Type 'demo()' for some demos, 'help()' for on-line help, or >> >> 'help.start()' for an HTML browser interface to help. >> >> Type 'q()' to quit R. >> >> >> >> [Workspace loaded from ~/.RData] >> >> >> >> > require(minfi) >> >> Loading required package: minfi >> >> Loading required package: BiocGenerics >> >> Loading required package: parallel >> >> >> >> Attaching package: æ ‹iocGenerics? >> >> The following objects are masked from 憄ackage:parallel? >> >> >> >> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, >> >> parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB >> >> >> >> The following object is masked from 憄ackage:stats? >> >> >> >> xtabs >> >> >> >> The following objects are masked from 憄ackage:base? >> >> >> >> anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, do.call, duplicated, eval, >> >> evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, >> >> paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, >> >> sapply, setdiff, sort, table, tapply, union, unique, unlist >> >> >> >> Loading required package: Biobase >> >> Welcome to Bioconductor >> >> >> >> Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, >> >> see 'citation("Biobase")', and for packages 'citation("pkgname")'. >> >> >> >> Loading required package: lattice >> >> Loading required package: GenomicRanges >> >> Loading required package: IRanges >> >> Loading required package: GenomeInfoDb >> >> Loading required package: Biostrings >> >> Loading required package: XVector >> >> Loading required package: bumphunter >> >> Loading required package: foreach >> >> foreach: simple, scalable parallel programming from Revolution Analytics >> >> Use Revolution R for scalability, fault tolerance and more. >> >> http://www.revolutionanalytics.com >> >> Loading required package: iterators >> >> Loading required package: locfit >> >> locfit 1.5-9.1 2013-03-22 >> >> > setwd("G:/Illumina/Brad/Minfi") >> >> > baseDir <- "G:/Illumina/Brad/Minfi/Scan Output" >> >> > targets <- read.450k.sheet(baseDir) >> >> [read.450k.sheet] Found the following CSV files: >> >> [1] "G:/Illumina/Brad/Minfi/Scan Output/SampleSheetSZ32.csv" >> >> > RGSet <- read.450k.exp(base = baseDir, targets = targets) >> >> > pd <- pData(RGSet) >> >> > pd[,1:4] >> >> Sample_Name Sample_Well Sample_Plate Sample_Group >> >> 8942300007_R02C01 CON1_CA32 B01 Plate1 CON_CA32 >> >> 8942300010_R06C01 CON2_CA32 B01 Plate1 CON_CA32 >> >> 8942297078_R06C01 CON3_CA32 F02 Plate1 CON_CA32 >> >> 8942300010_R01C01 CON4_CA32 E02 Plate1 CON_CA32 >> >> 8942300010_R05C01 CON5_CA32 A01 Plate1 CON_CA32 >> >> 8942297143_R06C02 CON6_CA32 H02 Plate1 CON_CA32 >> >> 8942297143_R06C01 CON7_CA32 B02 Plate1 CON_CA32 >> >> 8942297143_R01C02 CON8_CA32 C02 Plate1 CON_CA32 >> >> 8942300007_R01C01 SZ1_CA32 A01 Plate1 SZ_CA32 >> >> 8942300007_R03C01 SZ2_CA32 C01 Plate1 SZ_CA32 >> >> 8942297078_R03C02 SZ3_CA32 A01 Plate1 SZ_CA32 >> >> 8942300010_R02C01 SZ4_CA32 F02 Plate1 SZ_CA32 >> >> 8942300010_R02C02 SZ5_CA32 D01 Plate1 SZ_CA32 >> >> 8942297078_R01C01 SZ6_CA32 A02 Plate1 SZ_CA32 >> >> 8942297143_R04C01 SZ7_CA32 H01 Plate1 SZ_CA32 >> >> 8942297078_R06C02 SZ8_CA32 D01 Plate1 SZ_CA32 >> >> > >> >> > gRatioSet.quantile <- preprocessQuantile(RGSet, fixOutliers = TRUE, removeBadSamples = TRUE, badSampleCutoff = 10.5, quantileNormalize = TRUE, stratified = TRUE, mergeManifest = FALSE, sex = NULL) >> >> [preprocessQuantile] Mapping to genome. >> >> Loading required package: IlluminaHumanMethylation450kmanifest >> >> Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19 >> >> [preprocessQuantile] Fixing outliers. >> >> [preprocessQuantile] Quantile normalizing. >> >> > >> >> > GADBroad <- read.csv("GAD1LessBroad.csv") >> >> > GRSGADBroad <- as.vector(GADBroad) >> >> > Test <- GADBroad[1:1856,1] >> >> > MSetGADBroad <- as.vector(GADBroad[,1]) >> >> > GRQ <- gRatioSet.quantile[Test] >> >> > diagnosis <- pData(gRatioSet.quantile)$diagnosis >> >> > designMatrix <- model.matrix(~ diagnosis) >> >> > library(doParallel) >> >> > registerDoParallel(cores = 4) >> >> > dmrs <- bumphunter(GRQ, design = designMatrix, pickCutoff = TRUE, B=100, maxGap=500, smooth=TRUE, smoothFunction=locfitByCluster) >> >> [bumphunterEngine] Parallelizing using 4 workers/cores (backend: doParallelSNOW, version: 1.0.8). >> >> [bumphunterEngine] Computing coefficients. >> >> [bumphunterEngine] Smoothing coefficients. >> >> Error in { : task 1 failed - "unused argument (cutoffQ = 0.99)" >> >> >> - Brad >> >> ------------------------------ >> *From:* kasperdanielhansen@gmail.com [kasperdanielhansen@gmail.com] on >> behalf of Kasper Daniel Hansen [khansen@jhsph.edu] >> *Sent:* Tuesday, June 10, 2014 9:48 PM >> *To:* Brad Ruzicka [guest] >> *Cc:* bioconductor@r-project.org; Ruzicka, William B.,M.D. >> *Subject:* Re: [BioC] smoothing function in bumphunter in minfi >> >> I have been prompted on this off-list. Turns out I was reading the OP >> a bit too fast ... he is on R 3.0.3 which we no longer support (nor can I >> make changes to the relevant Bioconductor packages). So the solution is to >> upgrade to R-3.1. >> >> Hopefully that will fix the problem, otherwise get in touch. Whatever >> I have done would not have affected R 3.0.3. >> >> Best, >> Kasper >> >> >> On Wed, May 14, 2014 at 11:31 AM, Kasper Daniel Hansen <khansen@jhsph.edu>> > wrote: >> >>> This is a weirdly introduced error which we have fixed in the devel >>> branch. I was supposed to back port it into release, but I forgot. >>> >>> Kasper >>> >>> >>> On Wed, May 14, 2014 at 11:16 AM, Brad Ruzicka [guest] < >>> guest@bioconductor.org> wrote: >>> >>>> Hi there- >>>> I've been using bumphunter within minfi to analyze my HM450 dataset >>>> with good results, but I'm unable to use the smoothing function within >>>> bumphunter. When "smooth = TRUE" it gives the error: >>>> "Error in { : task 1 failed - "unused argument (cutoffQ = 0.99)"", even >>>> though I have not included cutoffQ in the script. >>>> >>>> The script below works fine with smooth = FALSE, but when set to true >>>> gives the above error: >>>> >>>> setwd("G:/Illumina/Brad/Minfi") >>>> baseDir <- "G:/Illumina/Brad/Minfi/Scan Output" >>>> targets <- read.450k.sheet(baseDir) >>>> RGSet <- read.450k.exp(base = baseDir, targets = targets) >>>> pd <- pData(RGSet) >>>> pd[,1:4] >>>> >>>> gRatioSet.quantile <- preprocessQuantile(RGSet, fixOutliers = TRUE, >>>> removeBadSamples = TRUE, badSampleCutoff = 10.5, quantileNormalize = TRUE, >>>> stratified = TRUE, mergeManifest = FALSE, sex = NULL) >>>> >>>> Age <- pData(gRatioSet.quantile)$age >>>> PMI <- pData(gRatioSet.quantile)$PMI >>>> diagnosis <- pData(gRatioSet.quantile)$diagnosis >>>> gender <- pData(gRatioSet.quantile)$gender >>>> >>>> designMatrix <- model.matrix(~ diagnosis + Age + PMI + gender) >>>> >>>> library(doParallel) >>>> registerDoParallel(cores = 4) >>>> dmrs <- bumphunter(gRatioSet.quantile, design = designMatrix, >>>> maxGap=500, pickCutoff = TRUE, smooth = TRUE, >>>> smoothFunction=locfitByCluster, B=1000) >>>> write.csv(dmrs$table, file = "GAD1BroadDMRsSZ3Test6.csv") >>>> >>>> Output of script: >>>> [read.450k.sheet] Found the following CSV files: >>>> [1] "G:/Illumina/Brad/Minfi/Scan Output/SampleSheetSZ32.csv" >>>> [preprocessQuantile] Mapping to genome. >>>> [preprocessQuantile] Fixing outliers. >>>> [preprocessQuantile] Quantile normalizing. >>>> [bumphunterEngine] Parallelizing using 4 workers/cores (backend: >>>> doParallelSNOW, version: 1.0.8). >>>> [bumphunterEngine] Computing coefficients. >>>> [bumphunterEngine] Smoothing coefficients. >>>> Error in { : task 1 failed - "unused argument (cutoffQ = 0.99)" >>>> >>>> Any ideas where my error is? >>>> Thanks, >>>> Brad >>>> >>>> -- output of sessionInfo(): >>>> >>>> > sessionInfo() >>>> R version 3.0.3 (2014-03-06) >>>> Platform: x86_64-w64-mingw32/x64 (64-bit) >>>> >>>> locale: >>>> [1] LC_COLLATE=English_United States.1252 >>>> [2] LC_CTYPE=English_United States.1252 >>>> [3] LC_MONETARY=English_United States.1252 >>>> [4] LC_NUMERIC=C >>>> [5] LC_TIME=English_United States.1252 >>>> >>>> attached base packages: >>>> [1] parallel stats graphics grDevices utils datasets methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] doParallel_1.0.8 >>>> [2] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 >>>> [3] IlluminaHumanMethylation450kmanifest_0.4.0 >>>> [4] doRNG_1.6 >>>> [5] rngtools_1.2.4 >>>> [6] pkgmaker_0.20 >>>> [7] registry_0.2 >>>> [8] minfi_1.8.9 >>>> [9] bumphunter_1.2.0 >>>> [10] locfit_1.5-9.1 >>>> [11] iterators_1.0.7 >>>> [12] foreach_1.4.2 >>>> [13] Biostrings_2.30.1 >>>> [14] GenomicRanges_1.14.4 >>>> [15] XVector_0.2.0 >>>> [16] IRanges_1.20.7 >>>> [17] reshape_0.8.5 >>>> [18] lattice_0.20-29 >>>> [19] Biobase_2.22.0 >>>> [20] BiocGenerics_0.8.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] annotate_1.40.1 AnnotationDbi_1.24.0 base64_1.1 >>>> [4] beanplot_1.1 codetools_0.2-8 compiler_3.0.3 >>>> [7] DBI_0.2-7 digest_0.6.4 genefilter_1.44.0 >>>> [10] grid_3.0.3 illuminaio_0.4.0 itertools_0.1-3 >>>> [13] limma_3.18.13 MASS_7.3-33 matrixStats_0.8.14 >>>> [16] mclust_4.3 multtest_2.18.0 nlme_3.1-117 >>>> [19] nor1mix_1.1-4 plyr_1.8.1 preprocessCore_1.24.0 >>>> [22] R.methodsS3_1.6.1 RColorBrewer_1.0-5 Rcpp_0.11.1 >>>> [25] RSQLite_0.11.4 siggenes_1.36.0 splines_3.0.3 >>>> [28] stats4_3.0.3 stringr_0.6.2 survival_2.37-7 >>>> [31] tools_3.0.3 XML_3.98-1.1 xtable_1.7-3 >>>> >>>> -- >>>> Sent via the guest posting facility at bioconductor.org. >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> >> > [[alternative HTML version deleted]]
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