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 | mashra...@yahoo.com
________________________________
From: Tian Yuan <champ4...@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 <champ4...@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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