[BioC] 'RankMerging' changes sample names

Alex [guest] guest at bioconductor.org
Sun Jul 27 13:33:26 CEST 2014


Hi, I'm working with .cel-files and after applying RankMerging function I loose my sample names.

>eset <- justRMA(filenames = list.celfiles(path=celpath, full.names=TRUE))     
>MergingSet <- RankMerging(eset ,"Spearman",weighted=TRUE)
> eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 22277 features, 3 samples 
  element names: exprs, se.exprs 
protocolData
  sampleNames: chrysin.cel luteolin.cel thiostrepton.cel
  varLabels: ScanDate
  varMetadata: labelDescription
phenoData
  sampleNames: chrysin.cel luteolin.cel thiostrepton.cel
  varLabels: sample
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: hthgu133a 
> MergingSet
ExpressionSet (storageMode: lockedEnvironment)
assayData: 22277 features, 3 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: 1 2 3
  varLabels: sample
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation:  

Please, could you help me?

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Russian_Russia.1251  LC_CTYPE=Russian_Russia.1251   
[3] LC_MONETARY=Russian_Russia.1251 LC_NUMERIC=C                   
[5] LC_TIME=Russian_Russia.1251    

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

other attached packages:
 [1] apcluster_1.3.5                GeneExpressionSignature_1.10.0
 [3] PGSEA_1.38.0                   annaffy_1.36.0                
 [5] KEGG.db_2.14.0                 GO.db_2.14.0                  
 [7] RSQLite_0.11.4                 DBI_0.2-7                     
 [9] AnnotationDbi_1.26.0           GenomeInfoDb_1.0.2            
[11] hthgu133acdf_2.14.0            affy_1.42.3                   
[13] Biobase_2.24.0                 BiocGenerics_0.10.0           

loaded via a namespace (and not attached):
[1] affyio_1.32.0         BiocInstaller_1.14.2  IRanges_1.22.9       
[4] preprocessCore_1.26.1 Rcpp_0.11.2           stats4_3.1.1         
[7] tools_3.1.1           zlibbioc_1.10.0      

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