[BioC] combineAffyBatch problem

Rifat A Hamoudi r.hamoudi at ucl.ac.uk
Mon Dec 15 22:14:51 CET 2008


Thanks Martin and Herve, the problem was gplots. I will be more careful
with this next time. I remember having problem with heatmap when using
aCGH as both had function with same name.

Problem is solved, thanks very much.

Rifat



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
>>> list Bioconductor at stat.math.ethz.ch
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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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