[BioC] combineAffyBatch problem

[Henrik Bengtsson]

On Sun, Dec 14, 2008 at 12:23 PM, Rifat A Hamoudi <r.hamoudi at ucl.ac.uk> wrote:
> 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 ?

Can't imagine anyone telling you not to - so, yes always make sure to
use the latest stable release of R - when you're at it get R v2.8.0
patched.  None of the BioC developers are using 2.7.x so you'll be
left behind if you use that.

My $.02

/Henrik

>
> 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 Perhaps some of your packages are out-of-date.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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