[BioC] Oligo package: paCalls question

[Alison Ziesel]

Hello all,

I’ve got very basic familiarity with the oligo package, but I’ve ran into a bit of trouble with the paCalls function. I’d like to restrict the probes in my eSet object to only those called present. Here’s what I’ve done thus far:

>library(“oligo”)
>library("pd.hugene.2.0.st”)
>allchips <- read.celfiles(“my list of cel files”)

>allchipspa <-paCalls(allchips, method=“PSDABG”, verbose=TRUE)
>present <- rownames(allchipspa)
>allchips_present <- exprs(allchips[present,])

Error in exprs(allchips[present, ]) : 
  error in evaluating the argument 'object' in selecting a method for function 'exprs': Error in orig[[nm]][i, , ..., drop = drop] : subscript out of bounds

Clearly my last line doesn’t do what I want it to do: filter the object allchips versus the list of present probes in the object present. I suppose at this point I should also confirm that my object allchipspa is just the present probes!  What’s the correct way to perform this filter step? I’d be grateful for any insight you may have.

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] pd.hugene.2.0.st_3.8.1 RSQLite_0.11.4         DBI_0.2-7              oligo_1.28.2          
 [5] Biostrings_2.32.1      XVector_0.4.0          IRanges_1.22.10        Biobase_2.24.0        
 [9] oligoClasses_1.26.0    BiocGenerics_0.10.0   

loaded via a namespace (and not attached):
 [1] affxparser_1.36.0     affyio_1.32.0         BiocInstaller_1.14.2  bit_1.1-12           
 [5] codetools_0.2-8       ff_2.2-13             foreach_1.4.2         GenomeInfoDb_1.0.2   
 [9] GenomicRanges_1.16.4  iterators_1.0.7       preprocessCore_1.26.1 splines_3.1.1        
[13] stats4_3.1.1          tools_3.1.1           zlibbioc_1.10.0  

alison

Alison Ziesel
Department of Ophthalmology, Emory University
aziesel at emory.edu