[BioC] Pipeline for listing phenoData in exprSet

[Sergii Ivakhno]

hello All,
I was wandering if you could possibly give me some suggestions with the 
following problem:
I would like to build a pipline which opens consequently exprset files 
(imported from GEO) and extracts and evaluates the phenoData labels 
(except the fields "sample" and "description").
The program is below:  the basic problem is that when you use 
names(pData(eset)), you obtain a character vector and you can
not use say  "phenonames <- names(pData(eset)); "eset$phenonames[2] or 
paste("eset",phenonames[2],sep="$")" (remember I need the vector in the 
first place to remove phenolabels "sample", "description").

Thanks a lot for advice!!
Best,
Sergii


Wellcome Trust Genome Campus
Hinxton, Cambridge, CB10 1SA, UK




dfg <-c("sample", "description");
files <-  dir(getwd(),".RData")
for (k in 1:length(files)){
load(files[k]);
pdateset <- names(pData(eset));
labels <- pdateset[-which(pdateset %in% dfg)];
for (m in 1:length(labels)){
teamp2 <- unique(paste("eset"    ,labels[m],sep="$"); 

teamp<-as.vector(teamp2);
for (i in 1:length(teamp)){
for (j in 2:length(teamp)){
if (i != j){
teamp1 <-  paste(teamp[i] ,teamp[j],sep="_")
teamp1 <-  paste(teamp1 ,files[k],sep="_")
temp <- ( as.character(eset$agent) == 
teamp[i])|(as.character(eset$agent) == teamp[j]);
tempeset <-eset[,temp];
design <- model.matrix(~factor(tempeset$agent));
fit <- lmFit(tempeset, design);
ebayes <- eBayes(fit);
sortebays <- sort.int(ebayes$t[,2], decreasing = TRUE, index.return = TRUE);
sortebays1 <- ebayes[sortebays$ix,];
save(sortebays1, file = paste(teamp1,c(".RData"),sep=""));
rm (sortebays,ebayes,temp,teamp1,tempeset,design,sortebays1,pdatesetlabels);
}      
}
}
}
}


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