[BioC] combineAffyBatch problem

[Rifat A Hamoudi]

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
>