Error in assay colnames when using readGEORawFile function in "minfi" package
0
0
Entering edit mode
moonkinwen • 0
@moonkinwen-11968
Last seen 8.0 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 • 1.3k views
ADD COMMENT

Login before adding your answer.

Traffic: 747 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6