Dear Benilton,

Yes, that fixed my problem. Thank you very much.

Best wishes,
Maria

On 23-01-2014 15:46, Benilton Carvalho wrote:
> Dear Maria,
>
> I'll make sure a fix is available soon.
>
> In the meantime, before doing anything with oligo (even loading), 
> please load the Biostrings package:
>
> library(Biostrings)
> require(oligoData)
> require(pd.huex.1.0.st.v2)
> data(affyExonFS)
> dabgP = paCalls(affyExonFS[, 1:2])
>
> this is the fix you're looking for.
>
> benilton
>
>
> 2014/1/23 Maria Rodrigo-Domingo [guest] <guest@bioconductor.org 
> <mailto:guest@bioconductor.org>>
>
>
>     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])
>
>
>     --
>     Sent via the guest posting facility at bioconductor.org
>     <http://bioconductor.org>.
>
>


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