[BioC] error when running paCalls

Benilton Carvalho beniltoncarvalho at gmail.com
Sun Sep 25 23:43:50 CEST 2011 

it's been fixed... wait for the next build cycle and get oligo 1.16.2.

b

2011/9/23 Benilton Carvalho <beniltoncarvalho at gmail.com>:
> 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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>
>
>
> --
> Successful people ask better questions, and as a result, they get
> better answers. (Tony Robbins)
>



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better answers. (Tony Robbins)

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