Question: ChAMP bailing before analysis complete
gravatar for schasse
3.0 years ago by
United States
schasse0 wrote:

I am running  R version 3.1.2 and launched champ.process() using the default command in the documentation as a first attempt. All the proper .cvs and iDat files are presumably in the home folder.

The command is accepted, the output folder is created, and the two .cvs files are read in when all of a sudden the program returns "Killed" and R quits; I find myself at the unix prompt.

Am I doing something fundamentally wrong or am I just too noob to get this?

> library(ChAMP)
Loading required package: minfi
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: âBiocGenericsâ

The following objects are masked from âpackage:parallelâ:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following object is masked from âpackage:statsâ:


The following objects are masked from âpackage:baseâ:

    anyDuplicated, append,, as.vector, cbind, colnames,, duplicated, eval, evalq, Filter, Find, get, intersect,
    is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,, pmin,, Position, rank, rbind, Reduce,,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unlist, unsplit

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: S4Vectors
Loading required package: stats4
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.
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1   2013-03-22
Loading required package: ChAMPdata
Loading required package: Illumina450ProbeVariants.db
Warning message:
replacing previous import by âRPMM::ebayesâ when loading âChAMPâ
> champ.process(fromIDAT = TRUE, fromFile = FALSE, directory = getwd(), resultsDir =
+ paste(getwd(), "resultsChamp20141210_01", sep = "/"), methValue = "B", filterDetP = TRUE,
+ detPcut = 0.01, filterXY = TRUE, removeDetP = 0, filterBeads = TRUE, beadCutoff =
+ 0.05, filterNoCG = FALSE, QCimages = TRUE, batchCorrect = TRUE, runSVD =
+ TRUE, studyInfo = FALSE, infoFactor = c(), norm = "BMIQ", adjust.method = "BH",
+ adjPVal = 0.05, runDMR = TRUE, runCNA = TRUE, plotBMIQ = TRUE, DMRpval = 0.05,
+ sampleCNA=TRUE,plotSample = TRUE,groupFreqPlots=TRUE,freqThreshold=0.3, bedFile
+ = FALSE, methProfile = FALSE, controlProfile = FALSE)
Loading data from /projects/sequence_analysis/vol1/schasse/workspace/IlluminaMethylUCSF/NIDA01_NIDA02
[read.450k.sheet] Found the following CSV files:
[1] "/projects/sequence_analysis/vol1/schasse/workspace/IlluminaMethylUCSF/NIDA01_NIDA02/NIDA01_02samplesheet.csv"
[2] "/projects/sequence_analysis/vol1/schasse/workspace/IlluminaMethylUCSF/NIDA01_NIDA02/playdata.csv"

sessionInfo() output


> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] ChAMP_1.4.0                       Illumina450ProbeVariants.db_1.1.1
 [3] ChAMPdata_1.1.2                   minfi_1.12.0
 [5] bumphunter_1.6.0                  locfit_1.5-9.1
 [7] iterators_1.0.7                   foreach_1.4.2
 [9] Biostrings_2.34.0                 XVector_0.6.0
[11] GenomicRanges_1.18.3              GenomeInfoDb_1.2.3
[13] IRanges_2.0.0                     S4Vectors_0.4.0
[15] lattice_0.20-29                   Biobase_2.26.0
[17] BiocGenerics_0.12.1

loaded via a namespace (and not attached):
 [1] annotate_1.44.0
 [2] AnnotationDbi_1.28.1
 [3] base64_1.1
 [4] beanplot_1.2
 [5] cluster_1.15.3
 [6] codetools_0.2-9
 [7] DBI_0.3.1
 [8] digest_0.6.6
 [9] DNAcopy_1.40.0
[10] doRNG_1.6
[11] genefilter_1.48.1
[12] grid_3.1.2
[13] IlluminaHumanMethylation450kmanifest_0.4.0
[14] illuminaio_0.8.0
[15] impute_1.40.0
[16] limma_3.22.1
[17] marray_1.44.0
[18] MASS_7.3-35
[19] Matrix_1.1-4
[20] matrixStats_0.12.2
[21] mclust_4.4
[22] mgcv_1.8-3
[23] multtest_2.22.0
[24] nlme_3.1-118
[25] nor1mix_1.2-0
[26] pkgmaker_0.22
[27] plyr_1.8.1
[28] preprocessCore_1.28.0
[29] quadprog_1.5-5
[30] R.methodsS3_1.6.1
[31] RColorBrewer_1.1-2
[32] Rcpp_0.11.3
[33] registry_0.2
[34] reshape_0.8.5
[35] rngtools_1.2.4
[36] RPMM_1.20
[37] RSQLite_1.0.0
[38] siggenes_1.40.0
[39] splines_3.1.2
[40] stringr_0.6.2
[41] survival_2.37-7
[42] sva_3.12.0
[43] tools_3.1.2
[44] wateRmelon_1.6.0
[45] XML_3.98-1.1
[46] xtable_1.7-4
[47] zlibbioc_1.12.0



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