[BioC] combineAffyBatch problem

Hervé Pagès hpages at fhcrc.org
Mon Dec 15 21:14:32 CET 2008


Hi Rifat,

As mentioned earlier, you need to upgrade to the current release version
of R + Bioconductor (i.e. R-2.8.0 + BioC 2.3). Older versions are not
supported. Thanks!

H.


Rifat A Hamoudi wrote:
> Hello,
>          I am still having same problem with combineAffyBatch but this
> time it is with R running on windows.
> 
> I would be grateful if someone can explain to me the meaning of the error.
> 
> I enclose my code and sessionInfo()
> 
> any help on this is greatly appreciated.
> 
> thanks
> 
> Rifat
> 
>> library(affy)# load affy lib
> Loading required package: Biobase
> Loading required package: tools
> 
> Welcome to Bioconductor
> 
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
> 
> Loading required package: affyio
> Loading required package: preprocessCore
>> library(gcrma)
> Loading required package: matchprobes
> Loading required package: splines
>> library(genefilter)
> Loading required package: survival
>> library(gplots)
> Loading required package: gtools
> Loading required package: gdata
> 
> Attaching package: 'gdata'
> 
> 
>         The following object(s) are masked from package:Biobase :
> 
>          combine
> 
> 
> Attaching package: 'gplots'
> 
> 
>         The following object(s) are masked from package:stats :
> 
>          lowess
> 
>> library(annotate)
> Loading required package: AnnotationDbi
> Loading required package: DBI
> Loading required package: RSQLite
> Loading required package: xtable
>> library(gsubfn)
> Loading required package: proto
>> library(limma)
>> library(hu6800probe)
>> library(hgu95av2probe)
>>
>>
>> f1 <- system.file("extdata", "118T1.cel", package = "matchprobes")
>> f2 <- system.file("extdata", "CL2001032020AA.cel", package = "matchprobes")
>>
>> pd1 <- new("AnnotatedDataFrame", data = data.frame(fromFile = I(f1),
> row.names = "f1"))
>> pd2 <- new("AnnotatedDataFrame", data = data.frame(fromFile = I(f2),
> row.names = "f2"))
>> x1 <- read.affybatch(filenames = f1, compress = TRUE, phenoData = pd1)
>> x2 <- read.affybatch(filenames = f2, compress = TRUE, phenoData = pd2)
>>
>> res <- combineAffyBatch(list(x1, x2), c("hu6800probe", "hgu95av2probe"),
> newcdf = "comb")
> package:hu6800probe     hu6800probe
> package:hgu95av2probe   hgu95av2probe
> 34431 unique probes in common
> Error in as.data.frame.default(x[[i]], optional = TRUE) :
>   cannot coerce class "AnnotatedDataFrame" into a data.frame
>> sessionInfo()
> R version 2.7.2 (2008-08-25)
> i386-pc-mingw32
> 
> locale:
> LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
> Kingdom.1252;LC_MONETARY=English_United
> Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
> 
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets 
> methods   base
> 
> other attached packages:
>  [1] hgu95av2probe_2.2.0  hu6800probe_2.2.0    limma_2.14.7        
> gsubfn_0.3-7
>  [5] proto_0.3-8          annotate_1.18.0      xtable_1.5-4        
> AnnotationDbi_1.2.2
>  [9] RSQLite_0.7-0        DBI_0.2-4            gplots_2.6.0        
> gdata_2.4.2
> [13] gtools_2.5.0         genefilter_1.20.1    survival_2.34-1     
> gcrma_2.12.1
> [17] matchprobes_1.12.1   affy_1.18.2          preprocessCore_1.2.1
> affyio_1.8.1
> [21] Biobase_2.0.1
> 
> 
> 
> 
>> Hi Marin,
>>
>> I tried update.packages() but still no luck. My sessionInfo() is as
>> follows:
>>
>>> sessionInfo()
>> R version 2.7.1 (2008-06-23)
>> i686-pc-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=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] splines   tools     stats     graphics  grDevices utils     datasets
>> [8] methods   base
>>
>> other attached packages:
>>  [1] hgu133plus2probe_2.2.0 hgu133plus2cdf_2.2.0   hgu133acdf_2.2.0
>>  [4] limma_2.14.6           gsubfn_0.3-7           proto_0.3-8
>>  [7] hgu133bprobe_2.2.0     hgu133aprobe_2.2.0     hgu133b.db_2.2.0
>> [10] hgu133a.db_2.2.0       annotate_1.18.0        xtable_1.5-4
>> [13] AnnotationDbi_1.2.2    RSQLite_0.7-1          DBI_0.2-4
>> [16] gplots_2.6.0           gdata_2.4.2            gtools_2.5.0
>> [19] genefilter_1.20.0      survival_2.34-1        gcrma_2.12.1
>> [22] matchprobes_1.12.0     affy_1.18.2            preprocessCore_1.2.1
>> [25] affyio_1.8.1           Biobase_2.0.1
>>
>> Do you think I should update to 2.8.0 ?
>>
>> Thanks
>>
>> Rifat
>>
>>
>> Hi --
>>
>> I cannot replicate this on my system -- the code you post below works
>> for me. Perhaps some of your packages are out-of-date. Try
>> update.packages() following the instructions here:
>>
>> http://bioconductor.org/docs/install
>>
>> This is my sessionInfo()
>>
>>> sessionInfo()
>> R version 2.8.0 Patched (2008-11-10 r46882)
>> x86_64-unknown-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=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] tools     stats     graphics  utils     datasets  grDevices methods
>> [8] base
>>
>> other attached packages:
>> [1] hu6800cdf_2.3.0      matchprobes_1.14.0   affy_1.20.0
>> [4] Biobase_2.2.1        limma_2.16.3         hgu133acdf_2.3.0
>> [7] hgu133plus2cdf_2.3.0
>>
>> loaded via a namespace (and not attached):
>> [1] affyio_1.10.1        preprocessCore_1.4.0
>>
>> What is yours?
>>
>> Martin
>>
>> "Rifat A Hamoudi" <r.hamoudi at ucl.ac.uk> writes:
>>
>>> Dear BioC users,
>>>
>>> I hope someone can help me. I am having problems running
>>> combineAffyBatch,
>>> when I run it I get the following error :
>>>
>>> Error in as.data.frame.default(x[[i]], optional = TRUE) :
>>>   cannot coerce class "AnnotatedDataFrame" into a data.frame
>>>
>>> I also run the script in matchprobe vignette but I still get this error.
>>>
>>> Can anyone help me to understand the source of this error and how to
>>> correct it?
>>>
>>> The code is below :
>>>
>>>
>>> thanks
>>>
>>>
>>> library(gsubfn)
>>> library(limma)
>>> library(matchprobes)
>>> library(hgu133acdf)
>>> library(hgu133plus2cdf)
>>> f1 <- system.file("extdata", "118T1.cel", package="matchprobes")
>>> f1
>>> f2 <- system.file("extdata", "CL2001032020AA.cel",
>>> package="matchprobes")
>>> pd1 <- new("AnnotatedDataFrame", data=data.frame(fromFile = I(f1),
>>> row.names="f1"))
>>> pd1
>>> pd1 <- new("AnnotatedDataFrame", data=data.frame(fromFile = I(f2),
>>> row.names="f2"))
>>> pd1 <- new("AnnotatedDataFrame", data=data.frame(fromFile = I(f1),
>>> row.names="f1"))
>>> pd2 <- new("AnnotatedDataFrame", data=data.frame(fromFile = I(f2),
>>> row.names="f2"))
>>> x1<-read.affybatch(filenames=f1, compress=TRUE, phenoData=pd1)
>>> x1
>>> x2<-read.affybatch(filenames=f2, compress=TRUE, phenoData=pd2)
>>> res<-combineAffyBatch(list(x1,x2), c("hu6800probe", "hgu95av2probe")
>>> , newcdf = "comb")
>>> res<-combineAffyBatch(list(x1,x2), c("hu6800probe", "hgu95av2probe"),
>>> newcdf="comb")
>>>
>>>> res<-combineAffyBatch(list(x1,x2), c("hu6800probe", "hgu95av2probe"),
>>> newcdf="comb")
>>> Loading required package: hu6800probe
>>> Loading required package: hgu95av2probe
>>> package:hu6800probe    hu6800probe
>>> package:hgu95av2probe  hgu95av2probe
>>> 34431 unique probes in common
>>> Error in as.data.frame.default(x[[i]], optional = TRUE) :
>>>   cannot coerce class "AnnotatedDataFrame" into a data.frame
>>> _______________________________________________ Bioconductor mailing
>>> list Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives:
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>> --
>> Martin Morgan
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M2 B169
>> Phone: (206) 667-2793
>>
>>
>>
> 
> _______________________________________________
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> 

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



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