Question

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

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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.

oligo oligo • 901 views

ADD COMMENT • link updated 10.2 years ago by Benilton Carvalho ★ 4.3k • written 10.2 years ago by Guest User ★ 13k

score 0 · Answer 1 · 2014-01-23

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> > > 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. > [[alternative HTML version deleted]]