Question: methyAnalysis error with example data
gravatar for Tom
2.2 years ago by
Tom10 wrote:



I'm working on illumina methylation array data. Focusing on the methylation pattern at 11p15.5, a imprinted region, I plan to use "methyAnalysis" to draw a heatmap by chromosome location.

Before actually analysing my data, I first tried the example codes and got the following error:

> library(methyAnalysis)
Loading required package: grid
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport,
    clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply,
    parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,,
    cbind, colnames,, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste,
    pmax,, pmin,, rank, rbind, rownames, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To
    cite Bioconductor, see 'citation("Biobase")', and for packages

Loading required package:
Loading required package: AnnotationDbi

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
No methods found in "GenomicRanges" for requests: overlapsAny
No methods found in "genoset" for requests: rowRanges, rowRanges<-, toGenomeOrder
Warning messages:
1: multiple methods tables found for 'colMeans' 
2: multiple methods tables found for 'colSums' 
3: multiple methods tables found for 'rowMeans' 
4: multiple methods tables found for 'rowSums' 
> data(exampleMethyGenoSet)
> heatmapByChromosome(exampleMethyGenoSet, gene='6493',
+                     genomicFeature='TxDb.Hsapiens.UCSC.hg19.knownGene', includeGeneBody=TRUE)
Error: Expectation Failed


Because it's just copy and paste of example code, I don't figure out what causes this error.

Can anyone help me with this error?




> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)

[1] C

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

other attached packages:
[1] methyAnalysis_1.14.0   AnnotationDbi_1.34.2 Biobase_2.32.0       GenomicRanges_1.24.0
[6] GenomeInfoDb_1.8.1   IRanges_2.6.0        S4Vectors_0.10.0     BiocGenerics_0.18.0 

loaded via a namespace (and not attached):
 [1] nlme_3.1-128                  bitops_1.0-6                  matrixStats_0.50.2            RColorBrewer_1.1-2           
 [5] httr_1.1.0                    tools_3.3.0                   doRNG_1.6                     nor1mix_1.2-1                
 [9] R6_2.1.2                      affyio_1.42.0                 rpart_4.1-10                  KernSmooth_2.23-15           
[13] Hmisc_3.17-4                  DBI_0.4-1                     Gviz_1.16.1                   mgcv_1.8-12                  
[17] colorspace_1.2-6              nnet_7.3-12                   methylumi_2.18.2              gridExtra_2.2.1              
[21] base64_2.0                    preprocessCore_1.34.0         chron_2.3-47                  pkgmaker_0.22                
[25] rtracklayer_1.32.0            scales_0.4.0                  genefilter_1.54.2             quadprog_1.5-5               
[29] affy_1.50.0                   stringr_1.0.0                 digest_0.6.9                  Rsamtools_1.24.0             
[33] foreign_0.8-66                illuminaio_0.14.0             siggenes_1.46.0               GEOquery_2.38.4              
[37] lumi_2.24.0                   XVector_0.12.0                htmltools_0.3.5               dichromat_2.0-0              
[41] BSgenome_1.40.0               ensembldb_1.4.2               limma_3.28.4                  RSQLite_1.0.0                
[45] shiny_0.13.2                  BiocInstaller_1.22.2          mclust_5.2                    BiocParallel_1.6.2           
[49] acepack_1.3-3.3               VariantAnnotation_1.18.1      RCurl_1.95-4.8                magrittr_1.5                 
[53] Formula_1.2-1                 Matrix_1.2-6                  Rcpp_0.12.5                   munsell_0.4.3                
[57] stringi_1.0-1                 nleqslv_3.0.1                 MASS_7.3-45                   genoset_1.28.2               
[61] SummarizedExperiment_1.2.2    zlibbioc_1.18.0               AnnotationHub_2.4.2           plyr_1.8.3                   
[65] bumphunter_1.12.0             minfi_1.18.2                  lattice_0.20-33               Biostrings_2.40.0            
[69] splines_3.3.0                 multtest_2.28.0               GenomicFeatures_1.24.2        annotate_1.50.0              
[73] locfit_1.5-9.1                beanplot_1.2                  rngtools_1.2.4                codetools_0.2-14             
[77] biomaRt_2.28.0                XML_3.98-1.4                  biovizBase_1.20.0             latticeExtra_0.6-28          
[81] data.table_1.9.6              httpuv_1.3.3                  foreach_1.4.3                 gtable_0.2.0                 
[85] openssl_0.9.3                 reshape_0.8.5                 ggplot2_2.1.0                 mime_0.4                     
[89] xtable_1.8-2                  survival_2.39-4               iterators_1.0.8               GenomicAlignments_1.8.0      
[93] registry_0.3                  cluster_2.0.4                 interactiveDisplayBase_1.10.3
ADD COMMENTlink written 2.2 years ago by Tom10
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