Error using oligo package with Affymetrix Arabidopsis Gene ST1.0 array data: paCalls() returns error 'vector would be too long'
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Peter Crisp ▴ 10
@peter-crisp-6309
Last seen 7.6 years ago
Australia
Hi All, Not sure if this is a BioC issue or a more general R issue but thought I'd start here. I am analyzing some Affymetrix Arabidopsis Gene 1.0 ST arrays using oligo and when I run paCalls() I get the error: Computing DABG calls... Error in 0:max(counts) : result would be too long a vector In addition: Warning message: In max(counts) : no non-missing arguments to max; returning -Inf Using the human data in the oligoData package seems to work fine... code reproduced below. Any ideas? I uploaded the .CEL.gz file at: https://dl.dropboxusercontent.com/u/73944704/GE_105GME_%28AraGene- 1_0-st%29.CEL.gz Thanks, Peter Australian National University -------CODE------- #The code that works: library(oligo) library(oligoData) data(affyGeneFS) affyGeneFS genePS <- rma(affyGeneFS, target = "core") dabgPS <- paCalls(affyGeneFS, 'PSDABG') #The code that fails (using the arabidopsis .CEL files) llibrary(oligo) affyGeneFS <- read.celfiles("celfilesAra/GE_105GME_(AraGene- 1_0-st).CEL") affyGeneFS genePS <- rma(affyGeneFS, target = "core") dabgPS <- paCalls(affyGeneFS, 'PSDABG') --------OUTPUT-------- > library(oligo) Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ‘package:stats’: xtabs The following objects are masked from ‘package:base’: anyDuplicated, as.data.frame, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Loading required package: oligoClasses Welcome to oligoClasses version 1.22.0 Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. ====================================================================== ======================= Welcome to oligo version 1.24.2 ====================================================================== ======================= > library(oligoData) > data(affyGeneFS) > affyGeneFS GeneFeatureSet (storageMode: lockedEnvironment) assayData: 1102500 features, 33 samples element names: exprs protocolData rowNames: TisMap_Brain_01_v1_WTGene1.CEL TisMap_Brain_02_v1_WTGene1.CEL ... TisMap_Thyroid_03_v1_WTGene1.CEL (33 total) varLabels: exprs dates varMetadata: labelDescription channel phenoData rowNames: TisMap_Brain_01_v1_WTGene1.CEL TisMap_Brain_02_v1_WTGene1.CEL ... TisMap_Thyroid_03_v1_WTGene1.CEL (33 total) varLabels: index varMetadata: labelDescription channel featureData: none experimentData: use 'experimentData(object)' Annotation: pd.hugene.1.0.st.v1 Loading required package: pd.hugene.1.0.st.v1 Loading required package: RSQLite Loading required package: DBI > genePS <- rma(affyGeneFS, target = "core") Background correcting Normalizing Calculating Expression > dabgPS <- paCalls(affyGeneFS, 'PSDABG') Computing DABG calls... OK > > library(oligo) > affyGeneFS <- read.celfiles("celfilesAra/GE_105GME_(AraGene- 1_0-st).CEL") Loading required package: pd.aragene.1.0.st Platform design info loaded. Reading in : celfilesAra/GE_105GME_(AraGene-1_0-st).CEL > affyGeneFS GeneFeatureSet (storageMode: lockedEnvironment) assayData: 1416100 features, 1 samples element names: exprs protocolData rowNames: GE_105GME_(AraGene-1_0-st).CEL varLabels: exprs dates varMetadata: labelDescription channel phenoData rowNames: GE_105GME_(AraGene-1_0-st).CEL varLabels: index varMetadata: labelDescription channel featureData: none experimentData: use 'experimentData(object)' Annotation: pd.aragene.1.0.st > genePS <- rma(affyGeneFS, target = "core") Background correcting Normalizing Calculating Expression > dabgPS <- paCalls(affyGeneFS, 'PSDABG') Computing DABG calls... Error in 0:max(counts) : result would be too long a vector In addition: Warning message: In max(counts) : no non-missing arguments to max; returning -Inf > > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] pd.aragene.1.0.st_3.8.0 pd.hugene.1.0.st.v1_3.8.0 RSQLite_0.11.4 [4] DBI_0.2-7 oligoData_1.8.0 oligo_1.24.2 [7] Biobase_2.20.1 oligoClasses_1.22.0 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] affxparser_1.32.3 affyio_1.28.0 BiocInstaller_1.10.3 Biostrings_2.28.0 [5] bit_1.1-11 codetools_0.2-8 ff_2.2-12 foreach_1.4.1 [9] GenomicRanges_1.12.5 IRanges_1.18.4 iterators_1.0.6 preprocessCore_1.22.0 [13] splines_3.0.1 stats4_3.0.1 tools_3.0.1 zlibbioc_1.6.0 > [[alternative HTML version deleted]]
oligo oligoClasses oligo oligoClasses • 1.2k views
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