Error in assay colnames when using readGEORawFile function in "minfi" package
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moonkinwen • 0
@moonkinwen-11968
Last seen 4.8 years ago

I used an example code readGEORawFile from "minfi" refrence manual and get en error

Any help will be valuable. Thanks in advance.

library(minfi)

gmset=readGEORawFile("GSE29290_Matrix_Signal.txt",Uname="Signal_A",Mname="Signal_B",sep="\t")
Error in FUN(X[[i]], ...) : 
  assay colnames() must be NULL or equal colData rownames()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936  LC_CTYPE=Chinese (Simplified)_China.936   
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C                              
[5] LC_TIME=Chinese (Simplified)_China.936    

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

other attached packages:
 [1] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 minfi_1.20.0                                      
 [3] bumphunter_1.14.0                                  locfit_1.5-9.1                                    
 [5] iterators_1.0.8                                    foreach_1.4.3                                     
 [7] Biostrings_2.42.1                                  XVector_0.14.0                                    
 [9] SummarizedExperiment_1.4.0                         GenomicRanges_1.26.1                              
[11] GenomeInfoDb_1.10.1                                IRanges_2.8.1                                     
[13] S4Vectors_0.12.1                                   Biobase_2.34.0                                    
[15] BiocGenerics_0.20.0                                BiocInstaller_1.24.0                              

loaded via a namespace (and not attached):
 [1] mclust_5.2               base64_2.0               Rcpp_0.12.8              lattice_0.20-34         
 [5] Rsamtools_1.26.1         digest_0.6.10            R6_2.2.0                 plyr_1.8.4              
 [9] RSQLite_1.1              httr_1.2.1               zlibbioc_1.20.0          GenomicFeatures_1.26.0  
[13] data.table_1.9.8         annotate_1.52.0          Matrix_1.2-7.1           preprocessCore_1.36.0   
[17] splines_3.3.2            BiocParallel_1.8.1       stringr_1.1.0            RCurl_1.95-4.8          
[21] biomaRt_2.30.0           rtracklayer_1.34.1       multtest_2.30.0          pkgmaker_0.22           
[25] openssl_0.9.5            GEOquery_2.40.0          quadprog_1.5-5           codetools_0.2-15        
[29] matrixStats_0.51.0       XML_3.98-1.5             reshape_0.8.6            GenomicAlignments_1.10.0
[33] MASS_7.3-45              bitops_1.0-6             grid_3.3.2               nlme_3.1-128            
[37] xtable_1.8-2             registry_0.3             DBI_0.5-1                magrittr_1.5            
[41] stringi_1.1.2            genefilter_1.56.0        doRNG_1.6                limma_3.30.6            
[45] nor1mix_1.2-2            RColorBrewer_1.1-2       siggenes_1.48.0          tools_3.3.2             
[49] illuminaio_0.16.0        rngtools_1.2.4           survival_2.40-1          AnnotationDbi_1.36.0    
[53] beanplot_1.2             memoise_1.0.0           

 
minfi methylation 450k • 687 views
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