[Bioc-devel] Problem with champ.load (Package ChAMP)
Mohammad Tanvir Ahamed
mashranga at yahoo.com
Thu Mar 30 05:58:44 CEST 2017
Hi,
I am writing the following command and get the following error.
Can you please look into the issue ?
> testDir=system.file("extdata",package="ChAMPdata")
> myLoad <- champ.load(testDir,arraytype="450K")
[===========================]
[<<<< ChAMP.LOAD START >>>>>]
-----------------------------
Loading data from C:/Program Files/R/R-3.4.0alpha/library/ChAMPdata/extdata
[read.metharray.sheet] Found the following CSV files:
[1] "C:/Program Files/R/R-3.4.0alpha/library/ChAMPdata/extdata/lung_test_set.csv"
Loading required package: IlluminaHumanMethylation450kmanifest
<< Read DataSet Success. >>
The fraction of failed positions per sample
(You may need to delete samples with high proportion of failed probes
):
Failed CpG Fraction.
C1 0.0013429122
C2 0.0022162171
C3 0.0003563249
C4 0.0002842360
T1 0.0003831007
T2 0.0011946152
T3 0.0014953286
T4 0.0015447610
Filtering probes with a detection p-value above 0.01 in one or more samples has removed 2728 probes from the analysis. If a large number of probes have been removed, ChAMP suggests you to identify potentially bad samples.
<< Filter DetP Done. >>
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'assayData' for signature '"RGChannelSetExtended"'
>
> sessionInfo()
R version 3.4.0 alpha (2017-03-28 r72427)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=Bangla_Bangladesh.1252 LC_CTYPE=Bangla_Bangladesh.1252 LC_MONETARY=Bangla_Bangladesh.1252
[4] LC_NUMERIC=C LC_TIME=Bangla_Bangladesh.1252
attached base packages:
[1] splines stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] IlluminaHumanMethylation450kmanifest_0.4.0 ChAMP_2.6.0
[3] IlluminaHumanMethylationEPICmanifest_0.3.0 Illumina450ProbeVariants.db_1.11.0
[5] DMRcate_1.11.2 DMRcatedata_1.10.1
[7] DSS_2.15.0 bsseq_1.11.0
[9] FEM_3.3.1 graph_1.53.0
[11] org.Hs.eg.db_3.4.0 impute_1.49.0
[13] igraph_1.0.1 corrplot_0.77
[15] marray_1.53.0 limma_3.31.19
[17] Matrix_1.2-9 AnnotationDbi_1.37.4
[19] ChAMPdata_2.6.0 minfi_1.21.5
[21] bumphunter_1.15.0 locfit_1.5-9.1
[23] iterators_1.0.8 foreach_1.4.3
[25] Biostrings_2.43.6 XVector_0.15.2
[27] SummarizedExperiment_1.5.7 DelayedArray_0.1.7
[29] matrixStats_0.51.0 Biobase_2.35.1
[31] GenomicRanges_1.27.23 GenomeInfoDb_1.11.9
[33] IRanges_2.9.19 S4Vectors_0.13.15
[35] BiocGenerics_0.21.3
loaded via a namespace (and not attached):
[1] R.utils_2.5.0 IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0
[3] RSQLite_1.1-2 htmlwidgets_0.8
[5] trimcluster_0.1-2 grid_3.4.0
[7] BiocParallel_1.9.5 munsell_0.4.3
[9] codetools_0.2-15 preprocessCore_1.37.0
[11] statmod_1.4.29 colorspace_1.3-2
[13] fastICA_1.2-0 BiocInstaller_1.25.3
[15] knitr_1.15.1 robustbase_0.92-7
[17] JADE_2.0-0 isva_1.9
[19] GenomeInfoDbData_0.99.0 biovizBase_1.23.2
[21] diptest_0.75-7 R6_2.2.0
[23] doParallel_1.0.10 illuminaio_0.17.0
[25] clue_0.3-53 flexmix_2.3-13
[27] bitops_1.0-6 reshape_0.8.6
[29] assertthat_0.1 IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0
[31] scales_0.4.1 nnet_7.3-12
[33] gtable_0.2.0 methylumi_2.21.0
[35] sva_3.23.0 ensembldb_1.99.12
[37] genefilter_1.57.0 rtracklayer_1.35.9
[39] lazyeval_0.2.0 acepack_1.4.1
[41] GEOquery_2.41.0 dichromat_2.0-0
[43] checkmate_1.8.2 yaml_2.1.14
[45] reshape2_1.4.2 GenomicFeatures_1.27.10
[47] backports_1.0.5 httpuv_1.3.3
[49] qvalue_2.7.0 Hmisc_4.0-2
[51] tools_3.4.0 nor1mix_1.2-2
[53] ggplot2_2.2.1 RColorBrewer_1.1-2
[55] DNAcopy_1.49.1 siggenes_1.49.0
[57] Rcpp_0.12.10 plyr_1.8.4
[59] base64enc_0.1-3 zlibbioc_1.21.0
[61] purrr_0.2.2 RCurl_1.95-4.8
[63] BiasedUrn_1.07 rpart_4.1-11
[65] openssl_0.9.6 viridis_0.4.0
[67] cluster_2.0.6 magrittr_1.5
[69] data.table_1.10.4 goseq_1.27.0
[71] mvtnorm_1.0-6 wateRmelon_1.19.3
[73] whisker_0.3-2 ProtGenerics_1.7.0
[75] missMethyl_1.9.1 RPMM_1.25
[77] mime_0.5 xtable_1.8-2
[79] XML_3.98-1.5 mclust_5.2.3
[81] gridExtra_2.2.1 compiler_3.4.0
[83] biomaRt_2.31.4 tibble_1.2
[85] R.oo_1.21.0 htmltools_0.3.5
[87] mgcv_1.8-17 Formula_1.2-1
[89] tidyr_0.6.1 DBI_0.6
[91] geneLenDataBase_1.11.0 MASS_7.3-47
[93] fpc_2.1-10 permute_0.9-4
[95] quadprog_1.5-5 R.methodsS3_1.7.1
[97] Gviz_1.19.3 RefFreeEWAS_2.1
[99] GenomicAlignments_1.11.12 registry_0.3
[101] foreign_0.8-67 plotly_4.5.6
[103] annotate_1.53.1 rngtools_1.2.4
[105] pkgmaker_0.22 multtest_2.31.0
[107] beanplot_1.2 ruv_0.9.6
[109] doRNG_1.6 stringr_1.2.0
[111] VariantAnnotation_1.21.17 digest_0.6.12
[113] base64_2.0 htmlTable_1.9
[115] dendextend_1.5.2 kernlab_0.9-25
[117] shiny_1.0.0 Rsamtools_1.27.13
[119] gtools_3.5.0 modeltools_0.2-21
[121] nlme_3.1-131 jsonlite_1.3
[123] viridisLite_0.2.0 BSgenome_1.43.7
[125] lattice_0.20-35 httr_1.2.1
[127] DEoptimR_1.0-8 survival_2.41-2
[129] GO.db_3.4.0 interactiveDisplayBase_1.13.0
[131] shinythemes_1.1.1 prabclus_2.2-6
[133] class_7.3-14 stringi_1.1.3
[135] AnnotationHub_2.7.14 latticeExtra_0.6-28
[137] memoise_1.0.0 dplyr_0.5.0
>
Tanvir Ahamed
Göteborg, Sweden | mashranga at yahoo.com
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