[BioC] ReadAffy - Error VECTOR_ELT() can only be applied to a 'list', not a 'char'

[Benilton Carvalho]

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b

On Jun 20, 2007, at 10:54 PM, Aedin Culhane wrote:

> Thanks Ben
> I did use biocLite() to do the update, so this is surprising.  affyiio
> should have been installed as a dependency of affy.  I used:
>
> source("http://www.bioconductor.org/biocLite.R")
> biocLite()
>
> I just installed affyio manually and now it works fine.
>
> Thanks for your help
> Aedin
>
>
> Ben Bolstad wrote:
>> You have a mismatch between your version of affy and your version of
>> affyio. You need 1.4.0 or later (the version released with BioC2.0).
>>
>> As a general rule people should not be mixing and matching packages
>> between different versions of BioC/R. It is always safest to re- 
>> install
>> the release using biocLite() or getBioC() rather than trying to  
>> install
>> packages manually and hoping it works.
>>
>> Best,
>>
>> Ben
>>
>>
>>
>>
>>
>>
>> On Wed, 2007-06-20 at 19:38 -0400, aedin culhane wrote:
>>
>>> Hi BioC,
>>> I am having problems getting ReadAffy to work on fc5. Any ideas?
>>> Thanks.
>>> Aedin
>>>
>>>> example(ReadAffy)
>>>
>>> RdAffy> if(require(affydata)){
>>> RdAffy+      celpath <- system.file("celfiles", package="affydata")
>>> RdAffy+      fns <- list.celfiles(path=celpath,full.names=TRUE)
>>> RdAffy+
>>> RdAffy+      cat("Reading files:\n",paste(fns,collapse="\n"),"\n")
>>> RdAffy+      ##read a binary celfile
>>> RdAffy+      abatch <- ReadAffy(filenames=fns[1])
>>> RdAffy+      ##read a text celfile
>>> RdAffy+      abatch <- ReadAffy(filenames=fns[2])
>>> RdAffy+      ##read all files in that dir
>>> RdAffy+      abatch <- ReadAffy(celfile.path=celpath)
>>> RdAffy+ }
>>> Loading required package: affydata
>>> Reading files:
>>>
>>> /home/aedin/R/i686-redhat-linux-gnu-library/2.5/affydata/celfiles/ 
>>> binary.cel
>>> /home/aedin/R/i686-redhat-linux-gnu-library/2.5/affydata/celfiles/ 
>>> text.cel
>>> Error in read.affybatch(filenames = l$filenames, phenoData = l 
>>> $phenoData,  :
>>>          VECTOR_ELT() can only be applied to a 'list', not a 'char'
>>>
>>>
>>>
>>>> sessionInfo()
>>> R version 2.5.0 (2007-04-23)
>>> i686-redhat-linux-gnu
>>>
>>> locale:
>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ 
>>> US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGE
>>>
>>> S=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHO 
>>> NE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFI
>>>                        CATION=C
>>>
>>> attached base packages:
>>> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"      
>>> "datasets"
>>> [7] "methods"   "base"
>>>
>>> other attached packages:
>>> affydata     affy   affyio  Biobase
>>> "1.11.2" "1.14.1"  "1.0.0" "1.14.0"
>>>
>>> _______________________________________________
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>>> gmane.science.biology.informatics.conductor
>>>
>
>
> -- 
> Aedín Culhane
> Research Associate in Prof. J Quackenbush Lab
> Harvard School of Public Health, Dana-Farber Cancer Institute
>
> 44 Binney Street, SM822
> Department of Biostatistics and Computational Biology,
> Dana-Farber Cancer Institute
> Boston, MA 02115
> USA
>
> Phone: +1 (617) 632 2468
> Fax:   +1 (617) 582 7760
> Email: aedin at jimmy.harvard.edu
> Web URL: http://www.hsph.harvard.edu/researchers/aculhane.html
>
> _______________________________________________
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