[BioC] fail combineAffyBatch for many files

[Wolfgang Huber]

Dear Oura

Please note that this is not a problem with "combineAffyBatch" but with 
"rma". I guess you are aware of 
http://bmbolstad.com/misc/ComputeRMAFAQ/ComputeRMAFAQ.html
and of the many discussions on this list on the topic of rma and memory 
size (Google will find them for you).

You are trying to use the function "justRMA" for something it is not 
intended to do, and this will not work.

Furthermore, what is causing (the unfortunately rather cryptic) error 
message that you get from justRMA is that you give it a parameter value 
for "cdfname" that is not what it expects: a character string with the 
name of a package,

Probably the easiest solution to your problem is to find a bigger computer.

  	Best wishes
	Wolfgang

----------------------------------------------------
Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber

Oura Tomonori ha scritto:
> 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
>  http://bmbolstad.com/misc/mixtureCDF/MixtureCDF.html
> 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)
>  i386-pc-mingw32
> 
>  locale:
>  LC_COLLATE=Japanese_Japan.932;LC_CTYPE=Japanese_Japan.932;LC_MONETARY=Japanese_Japan.932;LC_NUMERIC=C;LC_TIME=Japanese_Japan.932
> 
>  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
> IRanges_1.0.9
>   [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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