[BioC] combineAffyBatch problem
Rifat A Hamoudi
r.hamoudi at ucl.ac.uk
Mon Dec 15 21:03:09 CET 2008
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
>>>
>>
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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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