[BioC] combineAffyBatch problem

[Rifat A Hamoudi]

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 Perhaps some of your packages are out-of-date.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

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Phone: (206) 667-2793