Minfi RGChannelSet preprocessing error in assayDataElement
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Entering edit mode
lily • 0
@lily-11487
Last seen 3.8 years ago

As I process both my own data and the example data, I am able to create an RGset (RGChannelSet object). However, an error occurs when I attempt to create a MethylSet object with any of the preprocess commands. The error is: 

Error in `assayDataElement<-`(`*tmp*`, "Meth", validate = FALSE, value = c(22041,  : 
  unused argument (validate = FALSE)

 

Here is my code (using the example data):

library(minfi)

library(minfiData)

baseDir <- system.file("extdata", package = "minfiData")

targets <- read.metharray.sheet(baseDir) 

RGset <- read.metharray.exp(targets = targets) 

rawset <- preprocessRaw(RGset)

Error in `assayDataElement<-`(`*tmp*`, "Meth", validate = FALSE, value = c(22041,  : 
  unused argument (validate = FALSE)

 

traceback()

2: MethylSet(Meth = M, Unmeth = U, phenoData = phenoData(rgSet), 
       annotation = annotation(rgSet))
1: preprocessRaw(RGset)

 

sessionInfo()

R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] minfiData_0.14.0                                  
 [2] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
 [3] IlluminaHumanMethylation450kmanifest_0.4.0        
 [4] minfi_1.19.13                                     
 [5] bumphunter_1.12.0                                 
 [6] locfit_1.5-9.1                                    
 [7] iterators_1.0.8                                   
 [8] foreach_1.4.3                                     
 [9] Biostrings_2.40.2                                 
[10] XVector_0.12.1                                    
[11] SummarizedExperiment_1.2.3                        
[12] GenomicRanges_1.24.3                              
[13] GenomeInfoDb_1.8.7                                
[14] IRanges_2.6.1                                     
[15] S4Vectors_0.10.3                                  
[16] lattice_0.20-34                                   
[17] Biobase_2.32.0                                    
[18] BiocGenerics_0.18.0                               

loaded via a namespace (and not attached):
 [1] genefilter_1.54.2       splines_3.3.1          
 [3] beanplot_1.2            rtracklayer_1.32.2     
 [5] GenomicFeatures_1.24.5  chron_2.3-47           
 [7] XML_3.98-1.4            survival_2.39-5        
 [9] DBI_0.5-1               BiocParallel_1.6.6     
[11] RColorBrewer_1.1-2      registry_0.3           
[13] rngtools_1.2.4          doRNG_1.6              
[15] matrixStats_0.50.2      plyr_1.8.4             
[17] stringr_1.1.0           pkgmaker_0.22          
[19] zlibbioc_1.18.0         codetools_0.2-14       
[21] biomaRt_2.28.0          AnnotationDbi_1.34.4   
[23] illuminaio_0.14.0       preprocessCore_1.34.0  
[25] Rcpp_0.12.6             xtable_1.8-2           
[27] openssl_0.9.4           limma_3.28.21          
[29] base64_2.0              annotate_1.50.0        
[31] Rsamtools_1.24.0        digest_0.6.10          
[33] stringi_1.1.1           nor1mix_1.2-2          
[35] grid_3.3.1              quadprog_1.5-5         
[37] GEOquery_2.38.4         tools_3.3.1            
[39] bitops_1.0-6            magrittr_1.5           
[41] siggenes_1.46.0         RCurl_1.95-4.8         
[43] RSQLite_1.0.0           MASS_7.3-45            
[45] Matrix_1.2-7.1          data.table_1.9.6       
[47] httr_1.2.1              reshape_0.8.5          
[49] R6_2.1.3                mclust_5.2             
[51] GenomicAlignments_1.8.4 multtest_2.28.0        
[53] nlme_3.1-128    

minfi preprocessing error • 1000 views
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1
Entering edit mode
@kasper-daniel-hansen-2979
Last seen 6 months ago
United States
You're mixing minfi devel with Biobase stable. That does not work right now. You need to switch to Bioconductor devel. Best, Kasper (Sent from my phone.) > On Sep 15, 2016, at 18:07, lily [bioc] <noreply@bioconductor.org> wrote: > > Activity on a post you are following on support.bioconductor.org > User lily wrote Question: Minfi RGChannelSet preprocessing error in assayDataElement: > > As I process both my own data and the example data, I am able to create an RGset (RGChannelSet object). However, an error occurs when I attempt to create a MethylSet object with any of the preprocess commands. The error is: > > Error in `assayDataElement<-`(`*tmp*`, "Meth", validate = FALSE, value = c(22041, : > unused argument (validate = FALSE) > > > > Here is my code (using the example data): > > library(minfi) > library(minfiData) > > baseDir <- system.file("extdata", package = "minfiData") > > targets <- read.metharray.sheet(baseDir) > > RGset <- read.metharray.exp(targets = targets) > > rawset <- preprocessRaw(RGset) > > Error in `assayDataElement<-`(`*tmp*`, "Meth", validate = FALSE, value = c(22041, : > unused argument (validate = FALSE) > > > > traceback() > > 2: MethylSet(Meth = M, Unmeth = U, phenoData = phenoData(rgSet), > annotation = annotation(rgSet)) > 1: preprocessRaw(RGset) > > > > sessionInfo() > > R version 3.3.1 (2016-06-21) > Platform: x86_64-w64-mingw32/x64 (64-bit) > Running under: Windows >= 8 x64 (build 9200) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats4 parallel stats graphics grDevices utils > [7] datasets methods base > > other attached packages: > [1] minfiData_0.14.0 > [2] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 > [3] IlluminaHumanMethylation450kmanifest_0.4.0 > [4] minfi_1.19.13 > [5] bumphunter_1.12.0 > [6] locfit_1.5-9.1 > [7] iterators_1.0.8 > [8] foreach_1.4.3 > [9] Biostrings_2.40.2 > [10] XVector_0.12.1 > [11] SummarizedExperiment_1.2.3 > [12] GenomicRanges_1.24.3 > [13] GenomeInfoDb_1.8.7 > [14] IRanges_2.6.1 > [15] S4Vectors_0.10.3 > [16] lattice_0.20-34 > [17] Biobase_2.32.0 > [18] BiocGenerics_0.18.0 > > loaded via a namespace (and not attached): > [1] genefilter_1.54.2 splines_3.3.1 > [3] beanplot_1.2 rtracklayer_1.32.2 > [5] GenomicFeatures_1.24.5 chron_2.3-47 > [7] XML_3.98-1.4 survival_2.39-5 > [9] DBI_0.5-1 BiocParallel_1.6.6 > [11] RColorBrewer_1.1-2 registry_0.3 > [13] rngtools_1.2.4 doRNG_1.6 > [15] matrixStats_0.50.2 plyr_1.8.4 > [17] stringr_1.1.0 pkgmaker_0.22 > [19] zlibbioc_1.18.0 codetools_0.2-14 > [21] biomaRt_2.28.0 AnnotationDbi_1.34.4 > [23] illuminaio_0.14.0 preprocessCore_1.34.0 > [25] Rcpp_0.12.6 xtable_1.8-2 > [27] openssl_0.9.4 limma_3.28.21 > [29] base64_2.0 annotate_1.50.0 > [31] Rsamtools_1.24.0 digest_0.6.10 > [33] stringi_1.1.1 nor1mix_1.2-2 > [35] grid_3.3.1 quadprog_1.5-5 > [37] GEOquery_2.38.4 tools_3.3.1 > [39] bitops_1.0-6 magrittr_1.5 > [41] siggenes_1.46.0 RCurl_1.95-4.8 > [43] RSQLite_1.0.0 MASS_7.3-45 > [45] Matrix_1.2-7.1 data.table_1.9.6 > [47] httr_1.2.1 reshape_0.8.5 > [49] R6_2.1.3 mclust_5.2 > [51] GenomicAlignments_1.8.4 multtest_2.28.0 > [53] nlme_3.1-128 > > Post tags: minfi, preprocessing, error > > You may reply via email or visit Minfi RGChannelSet preprocessing error in assayDataElement
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