[BioC] paCalls() in oligo package fails for exon arrays (Error in normalizeSingleBracketSubscript)

[Maria Rodrigo-Domingo [guest]]

Hi,

The paCalls() function in oligo is failing for exon arrays. There seems to be a problem with normalizeSingleBracketSubscript().

I used the example from the user's manual, pages 28-29:

> require(oligoData)
> require(pd.huex.1.0.st.v2)
> data(affyExonFS)
> dabgP = paCalls(affyExonFS[, 1:2])
Computing DABG calls... Error in normalizeSingleBracketSubscript(i, x) :
  subscript contains NAs or out of bounds indices

I have also checked it for the gene array (dataset affyGeneFS) and it didn't work either. It seems to work for the expression dataset: affyExpressionFS, though. 

See output of sessionInfo() and traceback() below.

Any ideas of what could be wrong here?

Thanks a lot for your help!
Maria Rodrigo-Domingo
PhD student in Biostatistics
Aalborg University/Aalborg University Hospital


 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] pd.huex.1.0.st.v2_3.8.0 RSQLite_0.11.4          DBI_0.2-7              
[4] oligoData_1.8.0         oligo_1.26.0            Biobase_2.22.0         
[7] oligoClasses_1.24.0     BiocGenerics_0.8.0     

loaded via a namespace (and not attached):
 [1] affxparser_1.34.0     affyio_1.30.0         BiocInstaller_1.12.0 
 [4] Biostrings_2.30.1     bit_1.1-11            codetools_0.2-8      
 [7] ff_2.2-12             foreach_1.4.1         GenomicRanges_1.14.4 
[10] IRanges_1.20.6        iterators_1.0.6       preprocessCore_1.24.0
[13] splines_3.0.2         stats4_3.0.2          tools_3.0.2          
[16] XVector_0.2.0         zlibbioc_1.8.0    


> traceback()
18: stop("subscript contains NAs or out of bounds indices")
17: normalizeSingleBracketSubscript(i, x)
16: IRanges:::extractROWS(setNames(seq_along(x), names(x)), i)
15: IRanges:::extractROWS(setNames(seq_along(x), names(x)), i)
14: extractROWS(x[[j]], i)
13: extractROWS(x[[j]], i)
12: FUN(1L[[1L]], ...)
11: lapply(structure(seq_len(ncol(x)), names = names(x)), function(j) extractROWS(x[[j]], 
        i))
10: lapply(structure(seq_len(ncol(x)), names = names(x)), function(j) extractROWS(x[[j]], 
        i))
9: extractROWS(x, i)
8: extractROWS(x, i)
7: env[["pmSequence"]][idx, "sequence"]
6: env[["pmSequence"]][idx, "sequence"]
5: getRefDABG(x)
4: paFun(object)
3: .local(object, method, ..., verbose)
2: paCalls(affyExonFS[, 1:2])
1: paCalls(affyExonFS[, 1:2])
  

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