[BioC] error when running paCalls

[Valerie Obenchain]

Hi Lin,

Thank you for sending the files. I was able to reproduce your error. I'm
copying the package maintainer because I think you've identified a bug
in oligo.

Benilton, there is a problem in computePSDABG() when using ff files. I
believe the result of computeDABG() should be a matrix or data.frame. In
this
case it is a closed ff file. Using Lin's data which was attached to the
previous post,

library(oligo)
library(ff)

geneExp <- read.celfiles(filenames=c("GSM409113.CEL","GSM409114.CEL"))

## fails when method=SDABG :
> callps <- paCalls(geneExp,method="PSDABG")
Computing DABG calls... Error in log(paCalls(x, method = "DABG", verbose
= FALSE)) :
Non-numeric argument to mathematical function
In addition: Warning message:
In `[.ff_array`(exprs(x), tmp[["fid"]], , drop = FALSE) :
opening ff /media/valdrive/intensities-16fcfbb5.ff

## completes (with warning) when method=DABG (default) :
> callps <- paCalls(geneExp)
Computing DABG calls... OK
Warning message:
In `[.ff_array`(exprs(x), tmp[["fid"]], , drop = FALSE) :
opening ff /media/valdrive/intensities-16fcfbb5.ff

## The failure occurs in computePSDABG() at this line,
paProbe <- -log(paCalls(x, method="DABG", verbose=FALSE))

## Replicating this using Lin's data, we see the result is a closed fffile,

res <- paCalls(geneExp, method="DABG", verbose=FALSE)
> res <- paCalls(geneExp, method="DABG", verbose=FALSE)
Warning message:
In `[.ff_array`(exprs(x), tmp[["fid"]], , drop = FALSE) :
opening ff /media/valdrive/intensities-16fcfbb5.ff
> res
ff (closed) double length=1722986 (1722986) dim=c(861493,2) dimorder=c(1,2)

> -log(res)
Error in log(res) : Non-numeric argument to mathematical function

## I'm not sure if you want to recast the data or keep it in the file but
## some manipulation will need to take place before we can take the log,

open(res)
> res
ff (open) double length=1722986 (1722986) dim=c(861493,2) dimorder=c(1,2)
GSM409113.CEL GSM409114.CEL
116371 0.780254777 0.487261146
943979 0.003161222 0.242360379
493089 0.003161222 0.242360379
907039 0.056526208 0.149023638
1033309 0.011470282 0.043795620
653512 0.003099174 0.003099174
690769 0.035106383 0.067021277
997409 0.107438017 0.390495868
: : :


> logres <- -log(as.matrix(res[,]))
> head(logres)
GSM409113.CEL GSM409114.CEL
116371 0.2481348 0.7189551
943979 5.7567965 1.4173295
493089 5.7567965 1.4173295
907039 2.8730509 1.9036503
1033309 4.4679958 3.1282215
653512 5.7766198 5.7766198


Valerie





On 09/20/2011 06:49 PM, marco wrote:
> 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!!
>>>
>>>
>>
>