[BioC] subsetting an ExpressionSetIllumina object?

[Jenny Drnevich]

Oops - I forgot my sessionInfo()

 > sessionInfo()
R version 2.7.0 (2008-04-22)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

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

other attached packages:
  [1] beadarray_1.8.0       ath1121501probe_2.2.0 ath1121501cdf_2.2.0
  [4] ath1121501.db_2.2.0   affyQCReport_1.18.0   geneplotter_1.18.0
  [7] lattice_0.17-8        RColorBrewer_1.0-2    simpleaffy_2.16.0
[10] made4_1.14.0          ade4_1.4-7            affyPLM_1.16.0
[13] affycoretools_1.12.0  annaffy_1.12.0        KEGG.db_2.2.0
[16] gcrma_2.12.0          matchprobes_1.12.0    biomaRt_1.14.0
[19] RCurl_0.8-1           GOstats_2.6.0         Category_2.6.0
[22] genefilter_1.20.0     survival_2.34-1       RBGL_1.16.0
[25] annotate_1.18.0       xtable_1.5-2          GO.db_2.2.0
[28] AnnotationDbi_1.2.0   RSQLite_0.6-8         DBI_0.2-4
[31] graph_1.18.1          limma_2.14.1          affy_1.18.0
[34] preprocessCore_1.2.0  affyio_1.8.0          Biobase_2.0.1
[37] RWinEdt_1.8-0

loaded via a namespace (and not attached):
[1] cluster_1.11.10    grid_2.7.0         KernSmooth_2.22-22 XML_1.94-0.1
 >


At 01:36 PM 5/22/2008, Jenny Drnevich wrote:
>Hi,
>
>I have an ExpressionSetIllumina object with 12 samples. Is there a
>way to subset on the samples and create a new ExpressionSetIllumina
>object? The description of the ExpressionSetIllumina class has a
>combine() method for two ExpressionSetIllumina objects, and also has this:
>
>object[(index):
>Conducts subsetting of matrices and phenoData and reporterInfo components
># shouldn't this read object[(index)]: ?
>
>It appears this subsetting works on the features, not samples:
>
>  > dim(BS.bg.quant)
>Features  Samples
>     45281       12
>
>  > temp <- BS.bg.quant[1:6]
>  > dim(temp)
>Features  Samples
>         6       12
>
>Trying to subset on samples/columns like you can do for other
>ExpressionSet objects yields this:
>
>  > temp <- BS.bg.quant[,1:6]
>Error: subscript out of bounds
>
>
>Is there a way to subset on samples, or is there a reason why I
>shouldn't subset the object but instead create a new one using
>readBeadSummaryData?
>
>Thanks,
>Jenny
>
>
>Jenny Drnevich, Ph.D.
>
>Functional Genomics Bioinformatics Specialist
>W.M. Keck Center for Comparative and Functional Genomics
>Roy J. Carver Biotechnology Center
>University of Illinois, Urbana-Champaign
>
>330 ERML
>1201 W. Gregory Dr.
>Urbana, IL 61801
>USA
>
>ph: 217-244-7355
>fax: 217-265-5066
>e-mail: drnevich at illinois.edu
>         [[alternative HTML version deleted]]
>
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