[BioC] error when running paCalls

Fri Sep 23 19:07:54 CEST 2011

thansk for the report... will address the issue and get back to the
list once it's been fixed.

b

2011/9/23 Valerie Obenchain <vobencha at fhcrc.org>:
> 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!!
>>>>
>>>>
>>>
>>
>
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