Question: fail combineAffyBatch for many files
0
gravatar for Oura Tomonori
10.7 years ago by
Oura Tomonori30 wrote:
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
cdf matchprobes • 627 views
ADD COMMENTlink modified 10.7 years ago by Wolfgang Huber13k • written 10.7 years ago by Oura Tomonori30
Answer: fail combineAffyBatch for many files
0
gravatar for Wolfgang Huber
10.7 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
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),ro w.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),ro w.names="f2")) > > x2 <- read.affybatch(filenames=f2file,compress=FALSE,phenoData=pd2) > > > > res <- combineAffyBatch(list(x1,x2),c("hgu133aprobe","hgu133a2pro be"),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_MONETA RY=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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 10.7 years ago by Wolfgang Huber13k
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