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