Problem Subsetting ExpressionSet
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Entering edit mode
Tom Oates ▴ 60
@tom-oates-5703
Last seen 4.2 years ago

I am having trouble subsetting an ExpressionSet via an integer vector as follows:

I download an ExpressionSet from GEO to be object a1

pa1<-pData(a1)

And then grep the title column of pa1 to retain only a filtered part of the dataset

  title geo_accession
GSM475618 Uncontrolled astma GSM475618
GSM475619 Rhinitis GSM475619
GSM475621 Healthy C1 GSM47562
filInd <- c(grep("asthma",t(pa1["title"])),grep("Healthy",t(pa1["title"])))

Subsequent attempt to subset fails thus:

fa1<-a1
exprs(fa1) <- exprs(a1)[,filInd]

Returns

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

I am trying to adapt the code here

Any help is gratefully received

> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
[1] limma_3.30.13        GEOquery_2.40.0      Biobase_2.34.0      
[4] BiocGenerics_0.20.0  BiocInstaller_1.24.0

 

 

expressionset biobase bioconductor • 649 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States

The phenoData slot contains information about the columns of your ExpressionSet, not the rows.

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