[BioC] combineAffyBatch problem
Martin Morgan
mtmorgan at fhcrc.org
Mon Dec 15 21:27:15 CET 2008
Hi Rifat --
"Rifat A Hamoudi" <r.hamoudi at ucl.ac.uk> writes:
> 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
OK, I've been able to reproduce your problem, even with the most
recent Bioc. As a work-around, I think if you do not load the gplots
library, or load it at the very first location in the session, then
you will not have problems.
A fix will make it into the release and devel branches of Bioconductor
over the next several days. For any developers reading along: the
problem is that Biobase calls
do.call("combine", ...)
Since "combine' is quoted, R looks for the corresponding
symbol. Unfortunately, it starts the search at the .GlobalEnv and
finds it in gplots, rather starting in the package name space and
finding it in Biobase. The solution, I think, is to write
do.call(combine, ...)
Martin
> 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
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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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--
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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