[BioC] fail combineAffyBatch for many files

Oura Tomonori tomonori.oura at gmail.com
Tue Jan 20 06:43:37 CET 2009

Dear BioC,

I tested the combineAffyBatch function in the matchprobes library to
merge data from
HG-U133A and HG-U133Av2 GeneChips, which seemed to work well for small
number of arrays.

 > f1 <- list.files(path=dir1,".CEL",ignore.case=T,full.name=T)[1]
 > f1file <- list.files(path=dir1,".CEL",ignore.case=T,full.name=T)
 > pd1 <- new("AnnotatedDataFrame",data=data.frame(fromFile=I(f1),row.names="f1"))
 > x1 <- read.affybatch(filenames=f1file,compress=FALSE,phenoData=pd1)
 > f2 <- list.files(path=,".CEL",ignore.case=T,full.name=T)[1]
 > f2file <- list.files(path=dir2,".CEL",ignore.case=T,full.name=T)
 > pd2 <- new("AnnotatedDataFrame",data=data.frame(fromFile=I(f2),row.names="f2"))
 > x2 <- read.affybatch(filenames=f2file,compress=FALSE,phenoData=pd2)
 > res <- combineAffyBatch(list(x1,x2),c("hgu133aprobe","hgu133a2probe"),newcdf="comb")
 > exprs <- rma(res)

But for many arrays (44 and 60 arrays for each), memory allocation
error occured.

So I tried to use justRMA instead, but failed.

 > justRMA(filenames=c(f1,f2),cdfname=res$cdf)
 Error in checkSlotAssignment(object, name, value) :
  assignment of an object of class "AffyBatch" is not valid for slot
"cdfName" in an object of class "AffyBatch"; is(vaue, "character") is
not TRUE

I think creating mixture CDF environments such as
and using justRMA is the most probable solutions.
But I could not find how to create CDF environment by merging existing
CDF environments.

Thank's for any hints

 > sessionInfo()
 R version 2.8.1 (2008-12-22)


 attached base packages:
 [1] tools     stats     graphics  grDevices utils     datasets
methods   base

 other attached packages:
  [1] hgu133a2probe_2.3.0 hgu133aprobe_2.3.0  altcdfenvs_2.4.0
hypergraph_1.14.0   graph_1.20.0        Biostrings_2.10.15
  [8] makecdfenv_1.20.0   affyio_1.10.1       hgu133acdf_2.3.0
matchprobes_1.14.1  affy_1.20.0         Biobase_2.2.1

 loaded via a namespace (and not attached):
 [1] cluster_1.11.11      grid_2.8.1           lattice_0.17-17
Matrix_0.999375-17   preprocessCore_1.4.0

Tomonori Oura
Kyoto University School of Public Health
 Department of Biostatistics

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