but upgrading to R-2.8 + BioC 2.3 first is still highly recommended
:-)
Thanks!
H.
Martin Morgan wrote:
> 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=e
n_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_ID
ENTIFICATION=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=e
n_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_ID
ENTIFICATION=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:
>>>>
http://news.gmane.org/gmane.science.biology.informatics.conductor
>>> --
>>> 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
>>>
>>>
>>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>>
https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
--
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
