[Bioc-devel] Problem with champ.load ( wateRmelon::beadcount function )
Mohammad Tanvir Ahamed
mashranga at yahoo.com
Thu Mar 30 08:13:05 CEST 2017
Dear Yuan Tian,
Thank you very much for your mail .
I have already add a session info with the previous mail.
Problem arise in your script "champ.load.R" line 70 ( bc=beadcount(rgSet) ).
"beadcount" belongs to package "wateRmelon".
In "beadcount" function from line 3 (nb <- assayDataElement(x, "NBeads")) problem arise !!
I am using :
R version 3.4.0 alpha (2017-03-28 r72427)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Biobase (2.35.1), minfi (1.21.5), wateRmelon (1.19.3)
Yes you are right. minfi has change their class definition for "RGChannelSetExtended"
In my current version of R,
========================================
> getClass("RGChannelSetExtended")
Class "RGChannelSetExtended" [package "minfi"]
Slots:
Name: annotation colData assays NAMES elementMetadata metadata
Class: character DataFrame Assays character_OR_NULL DataFrame list
Extends:
Class "RGChannelSet", directly
Class "SummarizedExperiment", by class "RGChannelSet", distance 2
Class "Vector", by class "RGChannelSet", distance 3
Class "Annotated", by class "RGChannelSet", distance 4
========================================
but in
R version 3.3.3 (2017-03-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 14393)
minfi (1.20.2)
========================================
> getClass("RGChannelSetExtended")
Class "RGChannelSetExtended" [package "minfi"]
Slots:
Name: assayData phenoData featureData experimentData annotation protocolData .__classVersion__
Class: AssayData AnnotatedDataFrame AnnotatedDataFrame MIAxE character AnnotatedDataFrame Versions
Extends:
Class "RGChannelSet", directly
Class "eSet", by class "RGChannelSet", distance 2
Class "VersionedBiobase", by class "RGChannelSet", distance 3
Class "Versioned", by class "RGChannelSet", distance 4
>
========================================
No "assayData" is present in present version of minfi !!
Can anybody suggest how to solve the problem ?
Tanvir Ahamed
Göteborg, Sweden | mashranga at yahoo.com
________________________________
From: Tian Yuan <champ450k at gmail.com>
Sent: Thursday, 30 March 2017, 7:35
Subject: Re: Problem with champ.load
Below is my Test Code:
> testDir=system.file("extdata",package="ChAMPdata")
> myLoad <- champ.load(testDir,arraytype="450K")
[===========================]
[<<<< ChAMP.LOAD START >>>>>]
-----------------------------
Loading data from /home/tianyuan/R/x86_64-pc-linux-gnu-library/3.3/ChAMPdata/extdata
[read.metharray.sheet] Found the following CSV files:
[1] "/home/tianyuan/R/x86_64-pc-linux-gnu-library/3.3/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. >>
Filtering probes with a beadcount <3 in at least 5% of samples, has removed 9291 from the analysis.
<< Filter Beads Done. >>
Filtering non-cg probes, has removed 2959 from the analysis.
<< Filter NoCG Done. >>
Using general 450K SNP list for filtering.
Filtering probes with SNPs as identified in Zhou's Nucleic Acids Research Paper, 2016, has removed 49231 from the analysis.
<< Filter SNP Done. >>
Filtering probes that align to multiple locations as identified in Nordlund et al, has removed 7003 from the analysis.
<< Filter MultiHit Done. >>
Filtering probes on the X or Y chromosome has removed 9917 from the analysis.
<< Filter XY chromosome Done. >>
[Beta value is selected as output.]
Zeros in your dataset have been replaced with 0.000001
The analysis will be proceed with 404383 probes and 8 samples.
[<<<<< ChAMP.LOAD END >>>>>>]
[===========================]
[You may want to process champ.QC() next.]
Best
Yuan Tian
On Thu, 30 Mar 2017 at 12:02 Tian Yuan <champ450k at gmail.com> wrote:
Hello Tanvir:
>
>
>The error looks wired because seems no one reported that before, I guess it's a problem caused by version of Bioba, whihc is a bug in minfi, which is used by ChAMP. The problem is the latest version minfi is conflict with old version Biobase. The solution is replace your current Biobase package with the latest version (2.34), then it should be OK.
>
>Please try it see if it works. You are using Demo data, which should be correct as I tried now.
>
>
>Best
>Yuan Tian
>
wrote:
>
>Hi,
>>I am writing the following commend 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
>>
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