smoothing function in bumphunter in minfi
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Guest User ★ 12k
@guest-user-4897
Last seen 7.7 years ago
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.
minfi bumphunter minfi bumphunter • 1.3k views
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@kasper-daniel-hansen-2979
Last seen 10 months ago
United States
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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