[BioC] error when running paCalls

[marco]

hello everyone.
    here is my problem with code and output.
    translation from Chinese to English was given when needed.
    .gz of datafile were attached with this mail.
    Thanks a lot!!

    Lin Pei
### here is my code
library(oligo)
library(ff)
geneExp <- read.celfiles(filenames=c("GSM409113.CEL","GSM409114.CEL"))
esetps <- rma(geneExp,target="probeset")
callps <- paCalls(geneExp,method="PSDABG")

### here is the original output
> library(oligo)
载入需要的程辑包：oligoClasses
载入需要的程辑包：Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

================================================================================
Welcome to oligoClasses version 1.14.0
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
载入需要的程辑包：preprocessCore
Loading package bit1.1-7

package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2)

creators: bit bitwhich

coercion: as.logical as.integer as.bit as.bitwhich which

operator: ! & | xor != ==

querying: print length any all min max range sum summary

bit access: length<- [ [<- [[ [[<-

for more help type ?bit

Loading package ff2.2-3
- getOption("fftempdir")=="/tmp/RtmpsQZPOJ"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if
your system stalls on large writes

- getOption("ffbatchbytes")==16777216 -- consider a different value
for tuning your system

- getOption("ffmaxbytes")==536870912 -- consider a different value for
tuning your system

================================================================================
Welcome to oligo version 1.16.0
================================================================================
> library(ff)
载入需要的程辑包：tools
载入需要的程辑包：bit

载入程辑包：'bit'

The following object(s) are masked from 'package:base':

    xor

Attaching package ff

载入程辑包：'ff'

The following object(s) are masked from 'package:utils':

    write.csv, write.csv2

The following object(s) are masked from 'package:base':

    is.factor, is.ordered

================================================================================
Large dataset support for 'oligo/crlmm': Enabled
    - Probesets: 20,000
    - Samples..:    100
    - Path.....: /sdc1/linp/Data/GSE16558_RAW.tar_FILES
================================================================================
> geneExp <- read.celfiles(filenames=c("GSM409113.CEL","GSM409114.CEL"))
Loading required package: pd.hugene.1.0.st.v1
Loading required package: RSQLite
Loading required package: DBI
Platform design info loaded.
> esetps <- rma(geneExp,target="probeset")
Background correcting... OK
Normalizing... OK
Summarizing... OK
> callps <- paCalls(geneExp,method="PSDABG")
Computing DABG calls... 错误于log(paCalls(x, method = "DABG", verbose =
FALSE)) : (translation:error in)
  数学函数中用了非数值参数 ( translation:mathematical function use non-numeric argument)
此外: 警告信息：(translation:warnings)
In `[.ff_array`(exprs(x), tmp[["fid"]], , drop = FALSE) :
  opening ff /sdc1/linp/Data/GSE16558_RAW.tar_FILES/intensities-609fb008.ff


2011/9/21, Valerie Obenchain <vobencha at fhcrc.org>:
> Hello,
>
> There isn't enough information here to help answer your question.
> Please provide a small reproducible example of your error and the output
> of sessionInfo().
>
> Valerie
>
>
>
> On 09/20/2011 07:31 AM, marco wrote:
>> Hello Everyone
>>       i used the function paCalls in package oligo to calculated
>> detection pvalue for human gene 1.0 ST array at probeset level but
>> fail with the error message:
>>       "error in log(paCalls(x,method="DABG",verbose=FALSE))
>>        mathematical function used non-numeric parameter".( message was
>> translated from Chinese)
>>      my data is GSE16558 on GEO. Package ff was loaded.
>>      both read.celfiles() and rma() work fine.
>>      i used paCalls by paCalls(geneExp,method="PSDABG")
>>     Could you please give a hand?
>>     Thanks a lot!!
>>
>>
>
>


-- 
Lin Pei