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
>

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