I am trying to use ChAMP for the first time but I am experiencing a problem with importing data. I have a some EPIC idat files and a samplesheet.csv.
data.dir <- file.path("D:/data/idat/") myLoad <- champ.load(directory = data.dir, arraytype="EPIC")
The output I get is the following
[===========================] [<<<< ChAMP.LOAD START >>>>>] ----------------------------- Loading data from D:/data/idat [read.metharray.sheet] Found the following CSV files:  "D:/data/idat/Samplesheet.csv" << 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. NEU_P006_1 0.0009835634 NEU_P003_4 0.0013552857 NEU_P002_3 0.0007977022 NEU_P007_1 0.0007723051 NEU_P004_4 0.0007896213 NEU_P003_2 0.0014026168 NEU_P007_2 0.1024198892 NEU_P006_3 0.0012144468 NEU_P002_1 0.0008115553 NEU_P002_4 0.0008404157 NEU_P003_3 0.0008727394 NEU_P006_2 0.0009212249 NEU_P004_2 0.0008669673 NEU_P007_3 0.0007388270 NEU_P004_1 0.0010031885 NEU_P003_1 0.0015122865 Filtering probes with a detection p-value above 0.01 in one or more samples has removed 89843 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"'
I cannot get around this error message and therefore I cannot proceed with the analysis. The error happens even if I use the parameters
methValue = "M",detSamplecut = 0.11
To get the M values and get around the rejected sample.
The same dataset can be imported fine with minfi alone or with RnBeads.
Any help would be greatly appreciated.
Thank you in advance.
> sessionInfo() R version 3.4.0 (2017-04-21) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale:  LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C  LC_TIME=English_United Kingdom.1252 attached base packages:  splines stats4 parallel stats graphics grDevices utils datasets methods base other attached packages:  dendextend_1.5.2 qvalue_2.8.0 plyr_1.8.4 ChAMP_2.8.0  IlluminaHumanMethylationEPICmanifest_0.3.0 Illumina450ProbeVariants.db_1.12.0 DMRcate_1.12.0 DMRcatedata_1.12.0  DSS_2.16.0 bsseq_1.12.0 FEM_3.4.0 graph_1.54.0  org.Hs.eg.db_3.4.1 impute_1.50.0 igraph_1.0.1 corrplot_0.77  marray_1.54.0 limma_3.32.2 Matrix_1.2-10 AnnotationDbi_1.38.0  ChAMPdata_2.8.0 minfi_1.22.1 bumphunter_1.16.0 locfit_1.5-9.1  iterators_1.0.8 foreach_1.4.3 Biostrings_2.44.0 XVector_0.16.0  SummarizedExperiment_1.6.1 DelayedArray_0.2.1 matrixStats_0.52.2 Biobase_2.36.2  GenomicRanges_1.28.1 GenomeInfoDb_1.12.0 IRanges_2.10.0 S4Vectors_0.14.0  BiocGenerics_0.22.0 BiocInstaller_1.26.0 loaded via a namespace (and not attached):  R.utils_2.5.0 IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0 RSQLite_1.1-2  htmlwidgets_0.8 trimcluster_0.1-2 grid_3.4.0  BiocParallel_1.10.1 munsell_0.4.3 codetools_0.2-15  preprocessCore_1.38.0 statmod_1.4.29 colorspace_1.3-2  fastICA_1.2-0 knitr_1.15.1 robustbase_0.92-7  JADE_2.0-0 isva_1.9 GenomeInfoDbData_0.99.0  biovizBase_1.24.0 diptest_0.75-7 R6_2.2.0  doParallel_1.0.10 illuminaio_0.18.0 clue_0.3-53  AnnotationFilter_1.0.0 flexmix_2.3-14 bitops_1.0-6  reshape_0.8.6 assertthat_0.2.0 IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0  scales_0.4.1 nnet_7.3-12 gtable_0.2.0  methylumi_2.22.0 sva_3.24.0 ensembldb_2.0.1  genefilter_1.58.0 rtracklayer_1.36.0 lazyeval_0.2.0  acepack_1.4.1 GEOquery_2.42.0 dichromat_2.0-0  checkmate_1.8.2 yaml_2.1.14 reshape2_1.4.2  GenomicFeatures_1.28.0 backports_1.0.5 httpuv_1.3.3  Hmisc_4.0-3 tools_3.4.0 nor1mix_1.2-2  ggplot2_2.2.1 RColorBrewer_1.1-2 DNAcopy_1.50.0  siggenes_1.50.0 Rcpp_0.12.10 base64enc_0.1-3  zlibbioc_1.22.0 purrr_0.2.2 RCurl_1.95-4.8  BiasedUrn_1.07 rpart_4.1-11 openssl_0.9.6  viridis_0.4.0 cluster_2.0.6 magrittr_1.5  data.table_1.10.4 goseq_1.28.0 mvtnorm_1.0-6  wateRmelon_1.20.0 whisker_0.3-2 ProtGenerics_1.8.0  missMethyl_1.10.0 RPMM_1.25 mime_0.5  xtable_1.8-2 XML_3.98-1.7 mclust_5.2.3  gridExtra_2.2.1 compiler_3.4.0 biomaRt_2.32.0  tibble_1.3.0 R.oo_1.21.0 htmltools_0.3.6  mgcv_1.8-17 Formula_1.2-1 tidyr_0.6.2  DBI_0.6-1 geneLenDataBase_1.12.0 MASS_7.3-47  fpc_2.1-10 permute_0.9-4 quadprog_1.5-5  R.methodsS3_1.7.1 Gviz_1.20.0 RefFreeEWAS_2.1  GenomicAlignments_1.12.0 registry_0.3 IlluminaHumanMethylation450kmanifest_0.4.0  foreign_0.8-68 plotly_4.6.0 annotate_1.54.0  rngtools_1.2.4 pkgmaker_0.22 multtest_2.32.0  beanplot_1.2 ruv_0.9.6 doRNG_1.6.6  stringr_1.2.0 VariantAnnotation_1.22.0 digest_0.6.12  base64_2.0 htmlTable_1.9 kernlab_0.9-25  shiny_1.0.3 Rsamtools_1.28.0 gtools_3.5.0  modeltools_0.2-21 nlme_3.1-131 jsonlite_1.4  viridisLite_0.2.0 BSgenome_1.44.0 lattice_0.20-35  DEoptimR_1.0-8 httr_1.2.1 survival_2.41-3  GO.db_3.4.1 interactiveDisplayBase_1.14.0 shinythemes_1.1.1  prabclus_2.2-6 class_7.3-14 stringi_1.1.5  AnnotationHub_2.8.1 latticeExtra_0.6-28 memoise_1.1.0  dplyr_0.5.0
Your tags have everything except R :)
Very good point, I have rectified it. It's my first post! :)
Kudos! A very well written and well organized post.
I have a feeling that some of the dependencies of CHAMP is not fulfilled, most probably because they are old (or even not installed). Could you test your CHAMP installation on test data (see section 4 and 5.4)
Thank you for your reply!
I did run the test data from the ChAMPdata package and I get the exact same error message:
I am quite sure that it is a package related problem. But hard to point out which package with such a generic message. First, Try to re-install lumi and mehtylumi pacakges (in that order using biocondictor). If that fails to solve the problem, you may try to upgrade all the related pkgs using this:
When I load ChAMP I get the following warnings if this is of any help:
Another important point: Start a fresh session of R and see if the error repeats. The warn messages are because you have already methods with the same name from other packages, which are getting masked when you load CHAMP. This might create some conflicts. So, before doing anything, just try to run CHAMP in a freshly opened R. And do all the further test in the fresh session to avoid problems due to conflict with other packages.
I did reinstall lumi and methylumi as suggested and also started a new R session. The problem persists. Also, I have the latest versions of all packages and biocLite() does not update anything.
Interestingly, I installed ChAMP to another machine running Mac instead of Windows and I got the same error message.
Thank you very much in any case :)
It's really puzzling me now!!! Can you repost the error and sessionInfo on MAC?
Thank you very much for your persistence! :)
This is what I get on a Mac which is the same error I get on Windows. All packages (and R itself) are up-to-date:
The sessioninfo() result is huge and exceeds the 5000 character limit for the forum though so you can find it here https://pastebin.com/CnZByXjc
Did you check if it gives the same error with Champ test data?
Yes, I get the same error on Mac when using the ChAMP test data.
I have uploaded the Mac sessioninfo at https://pastebin.com/CnZByXjc
Interesting! Did you really run in a fresh R session? I see RnBeads_1.8.0 attached (16th entry), but is not used by CHAMP directly. Please try to run in a sandbox situation, else it will be really difficult to dissect the error.
PS: I installed and run on test data on my comp, and it runs fine!