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.
>
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