Error reading GEO files using minfi's readGEORawFile function
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dsperley • 0
@dsperley-7315
Last seen 6.5 years ago
United States

I'm trying to use minfi's readGEORawFile function to read in methylation data from the GEO  series GSE59091, but I keep getting the following error:

file<-"GSE59091_unmethylated_methylated_cor.txt"
GEO<-readGEORawFile(file,sep=" ",Uname="Unmethylated.signal",
+ Mname="Methylated.signal")
Read 485512 rows and 391 (of 586) columns from 1.054 GB file in 00:00:16
Error in FUN(X[[i]], ...) : 
  assay colnames() must be NULL or equal colData rownames()

sessionInfo:

R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin15.5.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
 [2] GEOquery_2.39.3                                   
 [3] RColorBrewer_1.1-2                                
 [4] IlluminaHumanMethylationEPICmanifest_0.3.0        
 [5] IlluminaHumanMethylation450kmanifest_0.4.0        
 [6] minfi_1.19.14                                     
 [7] bumphunter_1.13.1                                 
 [8] locfit_1.5-9.1                                    
 [9] iterators_1.0.8                                   
[10] foreach_1.4.3                                     
[11] Biostrings_2.41.4                                 
[12] XVector_0.13.7                                    
[13] SummarizedExperiment_1.3.82                       
[14] GenomicRanges_1.25.94                             
[15] GenomeInfoDb_1.9.12                               
[16] IRanges_2.7.15                                    
[17] S4Vectors_0.11.14                                 
[18] lattice_0.20-34                                   
[19] Biobase_2.33.3                                    
[20] BiocGenerics_0.19.2                               
[21] BiocInstaller_1.23.9                              

loaded via a namespace (and not attached):
 [1] mclust_5.2              base64_2.0              Rcpp_0.12.7            
 [4] Rsamtools_1.25.2        digest_0.6.10           R6_2.1.3               
 [7] plyr_1.8.4              chron_2.3-47            RSQLite_1.0.0          
[10] httr_1.2.1              zlibbioc_1.19.0         GenomicFeatures_1.25.16
[13] data.table_1.9.6        annotate_1.51.0         Matrix_1.2-7.1         
[16] preprocessCore_1.35.0   splines_3.3.1           BiocParallel_1.7.8     
[19] stringr_1.1.0           RCurl_1.95-4.8          biomaRt_2.29.2         
[22] rtracklayer_1.33.12     multtest_2.29.0         pkgmaker_0.22          
[25] openssl_0.9.4           quadprog_1.5-5          codetools_0.2-14       
[28] matrixStats_0.50.2      XML_3.98-1.4            reshape_0.8.5          
[31] GenomicAlignments_1.9.6 MASS_7.3-45             bitops_1.0-6           
[34] grid_3.3.1              nlme_3.1-128            xtable_1.8-2           
[37] registry_0.3            DBI_0.5-1               magrittr_1.5           
[40] stringi_1.1.1           genefilter_1.55.2       doRNG_1.6              
[43] limma_3.29.21           nor1mix_1.2-2           siggenes_1.47.0        
[46] tools_3.3.1             illuminaio_0.15.1       rngtools_1.2.4         
[49] survival_2.39-5         AnnotationDbi_1.35.4    beanplot_1.2           

 

 
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