Error subsetting eset
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sridhars • 0
@sridhars-11978
Last seen 7.3 years ago

Hello Bioconductor form,

 

I am trying to subset data in an eset, but am running into issues. Here's essentially what I'm attempting:

idx = c(1:10)

pData(eset) = pData(eset)[idx,]

exprs(eset) = exprs(eset)[,idx]

I can subset the pData slot fine, but when attempting the exprs slot subset, I get the following error:

Error in .validate_assayDataElementReplace(obj, value) : 
  object and replacement value have different dimensions

Here's my session info:

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] heatmap.plus_1.3     VennDiagram_1.6.17   futile.logger_1.4.1  rjson_0.2.15         networkD3_0.2.11     RCurl_1.95-4.8       bitops_1.0-6         RColorBrewer_1.1-2  
 [9] reshape2_1.4.1       rCharts_0.4.5        ggplot2_2.1.0        lattice_0.20-33      GEOquery_2.36.0      plotrix_3.6-2        GSEABase_1.32.0      graph_1.48.0        
[17] annotate_1.48.0      XML_3.98-1.4         AnnotationDbi_1.32.3 IRanges_2.4.8        S4Vectors_0.8.11     GSA_1.03             limma_3.26.9         affy_1.48.0         
[25] Biobase_2.30.0       BiocGenerics_0.16.1  gplots_3.0.1         devtools_1.11.1      GSVA_1.18.0          shiny_0.13.2        

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.5           gtools_3.5.0          digest_0.6.9          mime_0.4              R6_2.1.2              plyr_1.8.3            futile.options_1.0.0 
 [8] RSQLite_1.0.0         BiocInstaller_1.20.3  zlibbioc_1.16.0       gdata_2.17.0          whisker_0.3-2         DT_0.1.39             preprocessCore_1.32.0
[15] labeling_0.3          stringr_1.0.0         htmlwidgets_0.6       igraph_1.0.1          munsell_0.4.3         httpuv_1.3.3          htmltools_0.3.5      
[22] withr_1.0.1           jsonlite_0.9.20       xtable_1.8-2          gtable_0.2.0          DBI_0.4-1             magrittr_1.5          scales_0.4.0         
[29] KernSmooth_2.23-15    stringi_1.1.1         affyio_1.40.0         lambda.r_1.1.7        tools_3.2.2           RJSONIO_1.3-0         yaml_2.1.13          
[36] colorspace_1.2-6      caTools_1.17.1        memoise_1.0.0   

I've attempted the same operation using Biobase 2.30, as well as previous versions, and have not had this error pop up. Any input into how to work around this would be much appreciated.

 

Thanks,

Sri

software error • 892 views
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0
Entering edit mode
@james-w-macdonald-5106
Last seen 1 hour ago
United States

The idea behind the ExpressionSet is to provide an abstraction that works as if it were something less complicated. In this case, the idea is to make an ExpressionSet behave like a data.frame when subsetting. In other words, you can get what you want by just pretending your ExpressionSet is a data.frame, and acting accordingly.

eset.sub <- eset[,idx]
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