data.grs seems to have the correct number of samples (56). I'm including the output of str(data.grs), but please let me know if there's anything else I should be looking at. (As I may have mentioned, I am new to R.) > str(data.grs) Formal class 'GenomicRatioSet' [package "minfi"] with 6 slots ..@ preprocessMethod: chr(0) ..@ annotation : Named chr [1:2] "IlluminaHumanMethylation450k" "ilmn12.hg19" .. ..- attr(*, "names")= chr [1:2] "array" "annotation" ..@ exptData :Formal class 'SimpleList' [package "IRanges"] with 4 slots .. .. ..@ listData : list() .. .. ..@ elementType : chr "ANY" .. .. ..@ elementMetadata: NULL .. .. ..@ metadata : list() ..@ rowData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots .. .. ..@ seqnames :Formal class 'Rle' [package "IRanges"] with 4 slots .. .. .. .. ..@ values : Factor w/ 24 levels "chr1","chr2",..: 1 2 3 4 5 6 7 8 9 10 ... .. .. .. .. ..@ lengths : int [1:24] 46857 34810 25159 20464 24327 36611 30017 20950 9861 24388 ... .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. ..@ metadata : list() .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. ..@ start : int [1:485512] 15865 18827 29407 29425 29435 68849 69591 91550 135252 449076 ... .. .. .. .. ..@ width : int [1:485512] 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..@ NAMES : chr [1:485512] "cg13869341" "cg14008030" "cg12045430" "cg20826792" ... .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. ..@ metadata : list() .. .. ..@ strand :Formal class 'Rle' [package "IRanges"] with 4 slots .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*": 3 .. .. .. .. ..@ lengths : int 485512 .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. ..@ metadata : list() .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "IRanges"] with 6 slots .. .. .. .. ..@ rownames : NULL .. .. .. .. ..@ nrows : int 485512 .. .. .. .. ..@ listData : Named list() .. .. .. .. ..@ elementType : chr "ANY" .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. ..@ metadata : list() .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomicRanges"] with 4 slots .. .. .. .. ..@ seqnames : chr [1:24] "chr1" "chr2" "chr3" "chr4" ... .. .. .. .. ..@ seqlengths : int [1:24] NA NA NA NA NA NA NA NA NA NA ... .. .. .. .. ..@ is_circular: logi [1:24] NA NA NA NA NA NA ... .. .. .. .. ..@ genome : chr [1:24] "hg19" "hg19" "hg19" "hg19" ... .. .. ..@ metadata : list() ..@ colData :Formal class 'DataFrame' [package "IRanges"] with 6 slots .. .. ..@ rownames : chr [1:56] "TCGA.AB.2940.03A.01D.0742.05" "TCGA.AB.2944.03A.01D.0743.05" "TCGA.AB.2866.03A.01D.0741.05" "TCGA.AB.2871.03A.01D.0742.05" ... .. .. ..@ nrows : int 56 .. .. ..@ listData : Named list() .. .. ..@ elementType : chr "ANY" .. .. ..@ elementMetadata: NULL .. .. ..@ metadata : list() ..@ assays :Reference class 'ShallowSimpleListAssays' [package "GenomicRanges"] with 1 fields .. ..$ data:Formal class 'SimpleList' [package "IRanges"] with 4 slots .. .. .. ..@ listData :List of 2 .. .. .. .. ..$ Beta: num [1:485512, 1:56] 0.915 0.745 0.041 0.132 NA ... .. .. .. .. .. ..- attr(*, "dimnames")=List of 2 .. .. .. .. .. .. ..$ : chr [1:485512] "cg13869341" "cg14008030" "cg12045430" "cg20826792" ... .. .. .. .. .. .. ..$ : chr [1:56] "TCGA.AB.2940.03A.01D.0742.05" "TCGA.AB.2944.03A.01D.0743.05" "TCGA.AB.2866.03A.01D.0741.05" "TCGA.AB.2871.03A.01D.0742.05" ... .. .. .. .. ..$ M : num [1:485512, 1:56] 3.42 1.55 -4.55 -2.71 NA ... .. .. .. .. .. ..- attr(*, "dimnames")=List of 2 .. .. .. .. .. .. ..$ : chr [1:485512] "cg13869341" "cg14008030" "cg12045430" "cg20826792" ... .. .. .. .. .. .. ..$ : chr [1:56] "TCGA.AB.2940.03A.01D.0742.05" "TCGA.AB.2944.03A.01D.0743.05" "TCGA.AB.2866.03A.01D.0741.05" "TCGA.AB.2871.03A.01D.0742.05" ... .. .. .. ..@ elementType : chr "ANY" .. .. .. ..@ elementMetadata: NULL .. .. .. ..@ metadata : list() .. ..and 12 methods,> On 02/25/2014 10:43 AM, Kasper Daniel Hansen wrote: > This does not look nice: > > Warning message: > In regionFinder(x = beta, chr = chr, pos = pos, cluster = cluster, : > NAs found and removed. ind changed. > > I don't think the warnings > > Could not infer array name for file: > > are troublesome, but it is hard to read your output. > > Do you have the right number of samples in data.grs object? > > Kasper > > > On Tue, Feb 25, 2014 at 11:35 AM, Allegra Petti > <apetti@genome.wustl.edu <mailto:apetti@genome.wustl.edu="">> wrote: > > Kasper, > > Thanks for your message and the further clarification. I will try > using > the additional parameters you mentioned. To answer your question, > I only > have 56 samples, and the size of data.grs is 237.1 Mb. I get some > additional warning messages that I'm including again (below) in case > they are informative. > > Best, > Allegra > ________________________________________________________________ _______________ > From standard err: > > Warning messages: > 1: In > FUN(c("/gscmnt/gc3016/info/medseq/apetti/AMLrefractory/dmr.analy sis/IdatSampleSheet.csv", > : > Could not infer array name for file: > /gscmnt/gc3016/info/medseq/apetti/AMLrefractory/dmr.analysis/Ida tSampleSheet.csv > 2: In > FUN(c("/gscmnt/gc3016/info/medseq/apetti/AMLrefractory/dmr.analy sis/IdatSampleSheet.csv", > : > Could not infer slide name for file: > /gscmnt/gc3016/info/medseq/apetti/AMLrefractory/dmr.analysis/Ida tSampleSheet.csv > 3: In > FUN(c("/gscmnt/gc3016/info/medseq/apetti/AMLrefractory/dmr.analy sis/IdatSampleSheet.csv", > : > Could not infer array name for file: > /gscmnt/gc3016/info/medseq/apetti/AMLrefractory/dmr.analysis/Sam pleSheet140219.csv > 4: In > FUN(c("/gscmnt/gc3016/info/medseq/apetti/AMLrefractory/dmr.analy sis/IdatSampleSheet.csv", > : > Could not infer slide name for file: > /gscmnt/gc3016/info/medseq/apetti/AMLrefractory/dmr.analysis/Sam pleSheet140219.csv > [bumphunterEngine] Parallelizing using 12 workers/cores (backend: > doParallel, version: 1.0.6). > [bumphunterEngine] Computing coefficients. > [bumphunterEngine] Performing 100 permutations. > [bumphunterEngine] Computing marginal permutation p-values. > [bumphunterEngine] cutoff: 0.95 > [bumphunterEngine] Finding regions. > [bumphunterEngine] Found 6278 bumps. > [bumphunterEngine] Computing regions for each permutation. > > Warning messages: > 1: In regionFinder(x = beta, chr = chr, pos = pos, cluster = > cluster, : > NAs found and removed. ind changed. > 2: In FUN(newX[, i], ...) : NAs found and removed. ind changed. > 3: In FUN(newX[, i], ...) : NAs found and removed. ind changed. > 4: In FUN(newX[, i], ...) : NAs found and removed. ind changed. > > > > > > > Warning message: > Warning messages: > Warning messages: > Warning messages: > > Warning messages: > Warning messages: > > In regionFinder(x = beta, chr = chr, pos = pos, cluster = cluster, : > NAs found and removed. ind changed. > 1: In regionFinder(x = beta, chr = chr, pos = pos, cluster = > cluster, : > NAs found and removed. ind changed. > 1: In regionFinder(x = beta, chr = chr, pos = pos, cluster = > cluster, : > NAs found and removed. ind changed. > 1: In regionFinder(x = beta, chr = chr, pos = pos, cluster = > cluster, : > NAs found and removed. ind changed. > Warning messages: > beta2dmr.140224.err lines 84-106/115 92% > > > > > > > Warning message: > Warning messages: > Warning messages: > Warning messages: > > Warning messages: > Warning messages: > > In regionFinder(x = beta, chr = chr, pos = pos, cluster = cluster, : > NAs found and removed. ind changed. > 1: In regionFinder(x = beta, chr = chr, pos = pos, cluster = > cluster, : > NAs found and removed. ind changed. > 1: In regionFinder(x = beta, chr = chr, pos = pos, cluster = > cluster, : > NAs found and removed. ind changed. > 1: In regionFinder(x = beta, chr = chr, pos = pos, cluster = > cluster, : > NAs found and removed. ind changed. > Warning messages: > 1: In regionFinder(x = beta, chr = chr, pos = pos, cluster = > cluster, : > NAs found and removed. ind changed. > 1: In regionFinder(x = beta, chr = chr, pos = pos, cluster = > cluster, : > NAs found and removed. ind changed. > > > Warning messages: > 2: In FUN(newX[, i], ...) : NAs found and removed. ind changed. > Execution halted > ________________________________________________________________ _____________________ > From standard output: > > ------------------------------------------------------------ > Sender: LSF System <lsfadmin@blade14-2-15.gsc.wustl.edu> <mailto:lsfadmin@blade14-2-15.gsc.wustl.edu>> > Subject: Job 5344099: <beta2dmr> Exited > > Job <beta2dmr> was submitted from host <linus2091.gsc.wustl.edu> <http: linus2091.gsc.wustl.edu="">> by user > <apetti> in cluster <lsfcluster1>. > Job was executed on host(s) <12*blade14-2-15.gsc.wustl.edu > <http: blade14-2-15.gsc.wustl.edu="">>, in queue > <long>, as user <apetti> in cluster <lsfcluster1>. > </gscuser> was used as the home directory. > </gscuser> was used as the working > directory. > Started at Mon Feb 24 16:28:45 2014 > Results reported at Mon Feb 24 16:36:30 2014 > > Your job looked like: > > ------------------------------------------------------------ > # LSBATCH: User input > ~/gsc/R3.0.2/bin/Rscript beta2dmr_140220.r > ------------------------------------------------------------ > > TERM_MEMLIMIT: job killed after reaching LSF memory usage limit. > Exited with exit code 1. > > Resource usage summary: > > CPU time : 762.28 sec. > Max Memory : 69236 MB > Max Swap : 71263 MB > > Max Processes : 15 > Max Threads : 15 > > > On 02/24/2014 07:00 PM, Kasper Daniel Hansen wrote: > > One clarification: Jim's interpretation is for qCutoff. The cutoff > > argument is the actual cutoff. The call you are making says that any > > difference greater than 0.05 on the M scale is a possible bump. You > > can see from the output that there more than half the array inside a > > candidate bump. You probably want qCutoff or set type="Beta" or set > > cutoff to something bigger. > > > > This is really our fault for providing insanely crappy defaults. I > > will discuss with co-authors and we will change this. > > > > However, I am not sure I understand the memory blow up. How many > > samples do you have? What is the output of > > print(object.size(getBeta(data.grs)), units = "auto") > > > > Kasper > > > > > > On Mon, Feb 24, 2014 at 2:40 PM, Allegra A. Petti > > <apetti@genome.wustl.edu <mailto:apetti@genome.wustl.edu=""> > <mailto:apetti@genome.wustl.edu <mailto:apetti@genome.wustl.edu="">>> > wrote: > > > > Ah - thank you very much for the clarification!! I used 0.05 > > rather mindlessly because that's what the tutorial used. > > > > Best, > > Allegra > > _________________________________ > > Allegra A. Petti, Ph.D. > > > > The Genome Institute > > 4444 Forest Park Ave. > > St. Louis, MO 63108 > > apetti@genome.wustl.edu <mailto:apetti@genome.wustl.edu> > <mailto:apetti@genome.wustl.edu <mailto:apetti@genome.wustl.edu="">> > > allegra.conbrio@post.harvard.edu > <mailto:allegra.conbrio@post.harvard.edu> > > <mailto:allegra.conbrio@post.harvard.edu> <mailto:allegra.conbrio@post.harvard.edu>> > > > > On Feb 24, 2014, at 1:37 PM, "James W. MacDonald" > <jmacdon@uw.edu <mailto:jmacdon@uw.edu=""> > > <mailto:jmacdon@uw.edu <mailto:jmacdon@uw.edu="">>> wrote: > > > > > Hi Allegra, > > > > > > > > > On 2/24/2014 1:41 PM, Allegra Petti [guest] wrote: > > >> Dear All, > > >> > > >> I am trying to identify Differentially Methylated Regions > > (DMRs) using a tab-delimited file of beta values obtained with > > Illumina's 450k methylation arrays. I am using minfi and its > > implementation of bumphunter (development version 1.9.11). > > >> > > >> However, I run out of memory when I use a mere 100 > > permutations, and have tried different amounts of memory to no > > avail. Of further concern is the fact that the bumphunter > > reference (Jaffe, et al (2011) International J. of Epidemiology: > > 41:200-209) states that each permutation takes two hours (see p. > > 205). At that rate, a standard run with 1000 permutations would > > take over 83 days. > > >> > > >> My questions are as follows (code and output included below): > > >> 1. Is there a better way to run minfi/bumphunter, or specific > > resources I should allocate? (I am currently using parallel > > processing with four cores, and have tried various amounts > of memory.) > > >> 2. Does minfi/bumphunter include a non-permutation- based > method > > for estimating statistical significance? Jaffe et al state that > > they implemented a second, faster, p-value calculation following > > the method of Effron and Tibshirani (see p. 205). Does > anyone know > > if this method is implemented in minfi? > > >> 3. Is there a better method for identifying DMRs? (I am also > > experimenting with methyAnalysis, which has nice visualization > > options, but (a) is poorly documented and (b) surprisingly found > > no DMRs in my data set using default settings.) > > >> > > >> Many thanks in advance for any insight and/or suggestions! > > >> > > >> Sincerely, > > >> Allegra > > >> > _________________________________________________________________ > > >> Code: > > >> > > >> # This R script reads in a tab-delimited matrix of Beta > values > > (with a header line) > > >> # and finds differentially-methylated regions using minfi > > >> > > >> # sample command: bsub -oo beta2dmr.140224.out -e > > beta2dmr.140224.err -q long -M 16000000 -R 'select[type==LINUX64 > > && mem>16000] span[hosts=1] rusage[mem=16000]' -n 4 -J beta2dmr > > "~/gsc/R3.0.2/bin/Rscript beta2dmr_140220.r" > > >> > > >> library(minfi); # currently requires development version > 1.9.11 > > >> library(IlluminaHumanMethylation450kanno.ilmn12.hg19); # > Note: > > had to be installed manually > > >> library(foreach); # used for parallel processing > > >> library(doRNG); # is this actually used?? > > >> library(doParallel); # "backend" for foreach package > > >> registerDoParallel(cores = 4); > > >> > > >> #betas.frame <- > > > read.table(file="testbetas.txt",sep="\t",header=TRUE,na.strings= c(NA),row.names=1,quote=""); > > >> betas.frame <- > > > read.table(file="betas_140220.txt",sep="\t",header=TRUE,na.strin gs=c(NA),row.names=1,quote=""); > > >> betas <- as.matrix(betas.frame); # convert data frame to > matrix > > >> data.rs <http: data.rs=""> <http: data.rs=""> <- RatioSet(Beta = > > betas,annotation=c(array= "IlluminaHumanMethylation450k", > > annotation = "ilmn12.hg19")); # create RatioSet > > >> data.grs <- mapToGenomedata.rs <http: data.rs=""> > <http: data.rs="">); # create > > GenomicRatioSet > > >> sampleNamesdata.rs <http: data.rs=""> <http: data.rs="">); # > display the sample > > names (ie column headings) > > >> targets <- > > > read.450k.sheet('/gscmnt/gc3016/info/medseq/apetti/AMLrefractory /dmr.analysis',recursive=FALSE); > > # read Sample Sheet > > >> samples <- sampleNamesdata.rs <http: data.rs=""> > <http: data.rs="">); # get sample > > names (ie column headers) from input file of beta values > > >> j <- match(samples,targets$Sample); # get row indices from > > sample sheet that correspond to sample names (column headers) in > > beta value input file > > >> pheno <- targets$Sample_Group[j]; # extract corresponding > > phenotype (e.g. "tumor" or "normal") from Sample_Group column of > > Sample Sheet > > >> designMatrix <- model.matrix(~ pheno); # specify design > matrix > > for regression > > >> dmr <- bumphunter(data.grs, design = designMatrix, cutoff = > > 0.05, B=100); # run bumphunter with B permutations > > > > > > That's your problem ^^^^^^^^^^^^^^^^^^^^ > > > > > > You can interpret the cutoff argument this way; 'Select the > > bumps that are larger than the Xth quantile of all bumps in my > > data set'. By using 0.05, you are selecting almost all of the > > bumps in your data, which is not what you want to do. > > > > > > Instead, you want to use a cutoff of 0.95 or 0.99, which is > > 'Select the bumps that are larger than 95% or 99% of all the > bumps > > in my data'. Or to put it another way, you want to select the > > bumps that are big enough that they are likely to represent > > differential methylation, and ignore all the little bumps that > > likely arise by chance alone. > > > > > > Best, > > > > > > Jim > > > > > > > > >> save(dmr, file="dmr.minfi.100_140222"); > > >> > > >> > __________________________________________________________________ > > >> Standard Output: > > >> > > >> [1] "TCGA.AB.2940.03A.01D.0742.05" > "TCGA.AB.2944.03A.01D.0743.05" > > >> [3] "TCGA.AB.2866.03A.01D.0741.05" > "TCGA.AB.2871.03A.01D.0742.05" > > >> [5] "TCGA.AB.2934.03A.01D.0743.05" > "TCGA.AB.2807.03A.01D.0741.05" > > >> [7] "TCGA.AB.2809.03A.01D.0741.05" > "TCGA.AB.2984.03A.01D.0742.05" > > >> [9] "TCGA.AB.2921.03A.01D.0743.05" > "TCGA.AB.2952.03A.01D.0742.05" > > >> [11] "TCGA.AB.2829.03A.01D.0741.05" > "TCGA.AB.2901.03A.01D.0742.05" > > >> [13] "TCGA.AB.2827.03A.01D.0741.05" > "TCGA.AB.2884.03A.01D.0742.05" > > >> [15] "TCGA.AB.3011.03A.01D.0742.05" > "TCGA.AB.2878.03A.01D.0742.05" > > >> [17] "TCGA.AB.2933.03A.01D.0742.05" > "TCGA.AB.2843.03A.01D.0741.05" > > >> [19] "TCGA.AB.2814.03A.01D.0741.05" > "TCGA.AB.2856.03A.01D.0741.05" > > >> [21] "TCGA.AB.2855.03A.01D.0741.05" > "TCGA.AB.2919.03A.01D.0743.05" > > >> [23] "TCGA.AB.2967.03A.01D.0742.05" > "TCGA.AB.2817.03A.01D.0742.05" > > >> [25] "TCGA.AB.2887.03A.01D.0742.05" > "TCGA.AB.2894.03A.01D.0742.05" > > >> [27] "TCGA.AB.2895.03A.01D.0742.05" > "TCGA.AB.2947.03A.01D.0743.05" > > >> [29] "TCGA.AB.2930.03A.01D.0743.05" > "TCGA.AB.2896.03A.01D.0742.05" > > >> [31] "TCGA.AB.2983.03A.01D.0742.05" > "TCGA.AB.2945.03A.01D.0741.05" > > >> [33] "TCGA.AB.2918.03A.01D.0743.05" > "TCGA.AB.2928.03A.01D.0743.05" > > >> [35] "TCGA.AB.2979.03A.01D.0742.05" > "TCGA.AB.2969.03A.01D.0741.05" > > >> [37] "TCGA.AB.2891.03A.01D.0742.05" > "TCGA.AB.2971.03A.01D.0741.05" > > >> [39] "TCGA.AB.2964.03A.01D.0741.05" > "TCGA.AB.2835.03A.01D.0741.05" > > >> [41] "TCGA.AB.3002.03A.01D.0742.05" > "TCGA.AB.2853.03A.01D.0741.05" > > >> [43] "TCGA.AB.2836.03A.01D.0741.05" > "TCGA.AB.2909.03A.01D.0743.05" > > >> [45] "TCGA.AB.2932.03A.01D.0743.05" > "TCGA.AB.2926.03A.01D.0742.05" > > >> [47] "TCGA.AB.2826.03A.01D.0741.05" > "TCGA.AB.2911.03A.01D.0741.05" > > >> [49] "TCGA.AB.2920.03A.01D.0742.05" > "TCGA.AB.2917.03A.01D.0741.05" > > >> [51] "TCGA.AB.2869.03A.01D.0742.05" > "TCGA.AB.2873.03A.01D.0742.05" > > >> [53] "TCGA.AB.2879.03A.01D.0742.05" > "TCGA.AB.2831.03A.01D.0741.05" > > >> [55] "TCGA.AB.2816.03A.01D.0742.05" > "TCGA.AB.2990.03A.01D.0742.05" > > >> [read.450k.sheet] Found the following CSV files: > > >> [1] > > > "/gscmnt/gc3016/info/medseq/apetti/AMLrefractory/dmr.analysis/Id atSampleSheet.csv" > > >> [2] > > > "/gscmnt/gc3016/info/medseq/apetti/AMLrefractory/dmr.analysis/Sa mpleSheet140219.csv" > > >> > > >> ------------------------------------------------------------ > > >> Sender: LSF System <lsfadmin@blade14-4-11.gsc.wustl.edu> <mailto:lsfadmin@blade14-4-11.gsc.wustl.edu> > > <mailto:lsfadmin@blade14-4-11.gsc.wustl.edu> <mailto:lsfadmin@blade14-4-11.gsc.wustl.edu>>> > > >> Subject: Job 5329542: <beta2dmr> Exited > > >> > > >> Job <beta2dmr> was submitted from host > <linus2091.gsc.wustl.edu <http:="" linus2091.gsc.wustl.edu=""> > > <http: linus2091.gsc.wustl.edu="">> by user <apetti> in cluster > > <lsfcluster1>. > > >> Job was executed on host(s) <4*blade14-4-11.gsc.wustl.edu > <http: blade14-4-11.gsc.wustl.edu=""> > > <http: blade14-4-11.gsc.wustl.edu="">>, in queue <long>, as user > > <apetti> in cluster <lsfcluster1>. > > >> </gscuser> was used as the home directory. > > >> > > >> > __________________________________________________________________ > > >> Standard Error: > > >> > > >> Loading required package: methods > > >> 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': > > >> > > >> Filter, Find, Map, Position, Reduce, anyDuplicated, > append, > > >> as.data.frame, as.vector, cbind, colnames, duplicated, > > eval, evalq, > > >> get, intersect, is.unsorted, lapply, mapply, match, mget, > > order, > > >> paste, pmax, pmax.int <http: pmax.int=""> > <http: pmax.int="">, pmin, pmin.int <http: pmin.int=""> > > <http: pmin.int="">, rank, rbind, rep.int <http: rep.int=""> > <http: 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: XVector > > >> Loading required package: Biostrings > > >> Loading required package: bumphunter > > >> Loading required package: foreach > > >> Loading required package: iterators > > >> Loading required package: locfit > > >> locfit 1.5-9.1 2013-03-22 > > >> > > >> Attaching package: 'locfit' > > >> > > >> The following objects are masked from > 'package:GenomicRanges': > > >> > > >> left, right > > >> > > >> Loading required package: rngtools > > >> Loading required package: pkgmaker > > >> Loading required package: registry > > >> > > >> Attaching package: 'pkgmaker' > > >> > > >> The following object is masked from 'package:IRanges': > > >> > > >> new2 > > >> > > >> Warning messages: > > >> 1: In > > > FUN(c("/gscmnt/gc3016/info/medseq/apetti/AMLrefractory/dmr.analy sis/IdatSampleSheet.csv", > > : > > >> Could not infer array name for file: > > > /gscmnt/gc3016/info/medseq/apetti/AMLrefractory/dmr.analysis/Ida tSampleSheet.csv > > >> 2: In > > > FUN(c("/gscmnt/gc3016/info/medseq/apetti/AMLrefractory/dmr.analy sis/IdatSampleSheet.csv", > > : > > >> Could not infer slide name for file: > > > /gscmnt/gc3016/info/medseq/apetti/AMLrefractory/dmr.analysis/Ida tSampleSheet.csv > > >> 3: In > > > FUN(c("/gscmnt/gc3016/info/medseq/apetti/AMLrefractory/dmr.analy sis/IdatSampleSheet.csv", > > : > > >> Could not infer array name for file: > > > /gscmnt/gc3016/info/medseq/apetti/AMLrefractory/dmr.analysis/Sam pleSheet140219.csv > > >> 4: In > > > FUN(c("/gscmnt/gc3016/info/medseq/apetti/AMLrefractory/dmr.analy sis/IdatSampleSheet.csv", > > : > > >> Could not infer slide name for file: > > > /gscmnt/gc3016/info/medseq/apetti/AMLrefractory/dmr.analysis/Sam pleSheet140219.csv > > >> [bumphunterEngine] Parallelizing using 4 workers/cores > > (backend: doParallel, version: 1.0.6). > > >> [bumphunterEngine] Computing coefficients. > > >> [bumphunterEngine] Performing 100 permutations. > > >> [bumphunterEngine] Computing marginal permutation p-values. > > >> [bumphunterEngine] cutoff: 0.05 > > >> [bumphunterEngine] Finding regions. > > >> [bumphunterEngine] Found 233469 bumps. > > >> [bumphunterEngine] Computing regions for each permutation. > > >> > > >> Warning message: > > >> In regionFinder(x = beta, chr = chr, pos = pos, cluster = > > cluster, : > > >> NAs found and removed. ind changed. > > >> Execution halted > > >> > > >> > > >> -- output of sessionInfo(): > > >> > > >> R version 3.0.2 (2013-09-25) > > >> Platform: x86_64-unknown-linux-gnu (64-bit) > > >> > > >> locale: > > >> [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C > > >> [3] LC_TIME=en_US.utf8 LC_COLLATE=C > > >> [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 > > >> [7] LC_PAPER=en_US.utf8 LC_NAME=C > > >> [9] LC_ADDRESS=C LC_TELEPHONE=C > > >> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C > > >> > > >> attached base packages: > > >> [1] parallel stats graphics grDevices utils > datasets > > methods > > >> [8] base > > >> > > >> other attached packages: > > >> [1] doParallel_1.0.6 > > >> [2] doRNG_1.5.5 > > >> [3] rngtools_1.2.3 > > >> [4] pkgmaker_0.17.4 > > >> [5] registry_0.2 > > >> [6] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 > > >> [7] minfi_1.9.11 > > >> [8] bumphunter_1.2.0 > > >> [9] locfit_1.5-9.1 > > >> [10] iterators_1.0.6 > > >> [11] foreach_1.4.1 > > >> [12] Biostrings_2.30.1 > > >> [13] GenomicRanges_1.14.4 > > >> [14] XVector_0.2.0 > > >> [15] IRanges_1.20.6 > > >> [16] lattice_0.20-24 > > >> [17] Biobase_2.22.0 > > >> [18] BiocGenerics_0.8.0 > > >> > > >> loaded via a namespace (and not attached): > > >> [1] AnnotationDbi_1.24.0 DBI_0.2-7 MASS_7.3-29 > > >> [4] R.methodsS3_1.6.1 RColorBrewer_1.0-5 RSQLite_0.11.4 > > >> [7] XML_3.98-1.1 annotate_1.40.0 beanplot_1.1 > > >> [10] codetools_0.2-8 digest_0.6.4 genefilter_1.44.0 > > >> [13] grid_3.0.2 illuminaio_0.2.0 itertools_0.1-1 > > >> [16] limma_3.18.4 matrixStats_0.8.14 mclust_4.2 > > >> [19] multtest_2.18.0 nlme_3.1-113 nor1mix_1.1-4 > > >> [22] preprocessCore_1.24.0 reshape_0.8.4 siggenes_1.36.0 > > >> [25] splines_3.0.2 stats4_3.0.2 stringr_0.6.2 > > >> [28] survival_2.37-7 tools_3.0.2 xtable_1.7-1 > > >> > > >> -- > > >> Sent via the guest posting facility at bioconductor.org > <http: bioconductor.org=""> > > <http: bioconductor.org="">. > > >> > > >> _______________________________________________ > > >> Bioconductor mailing list > > >> Bioconductor@r-project.org > <mailto:bioconductor@r-project.org> > <mailto:bioconductor@r-project.org> <mailto:bioconductor@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 > > > > > > > > ____ > > This email message is a private communication. The information > > transmitted, including attachments, is intended only for the > > person or entity to which it is addressed and may contain > > confidential, privileged, and/or proprietary material. Any > review, > > duplication, retransmission, distribution, or other use of, or > > taking of any action in reliance upon, this information by > persons > > or entities other than the intended recipient is unauthorized by > > the sender and is prohibited. If you have received this > message in > > error, please contact the sender immediately by return email and > > delete the original message from all computer systems. Thank > you. > > > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > <mailto:bioconductor@r-project.org> <mailto:bioconductor@r-project.org>> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > ____ > This email message is a private communication. The information > transmitted, including attachments, is intended only for the > person or entity to which it is addressed and may contain > confidential, privileged, and/or proprietary material. Any review, > duplication, retransmission, distribution, or other use of, or > taking of any action in reliance upon, this information by persons > or entities other than the intended recipient is unauthorized by > the sender and is prohibited. 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If you have received this message in error, please contact the sender immediately by return email and delete the original message from all computer systems. Thank you. [[alternative HTML version deleted]]