Hi, Alex.  You are definitely thinking correctly that you want to be using
ExpressionSets.  I would focus your attention on learning to construct an
ExpressionSet for each case you outline.

Sean

On Jul 23, 2010 10:12 AM, "Alex Levitchi" <alex.levitchi@cbm.fvg.it> wrote:

Dear Bioconductors,
I am working on the development of a tool which use to download microarray
data and then make the connection to Bioconductor annotation packages.
My specific answer is about the way to manage downloading different kinds of
microarrays, which can be:
- GSE
- several GSMs
- users data (excel or tab delimiter file).
I use GEOquery package.
My tool works fine if I am using just GSE file, which has a good structure
and I know how to extract expression values, platform (GPL) and samples
names.

> gse=getGEO(idata,GSEMatrix=TRUE)
>columns=c('title','type','source_name_ch1','platform_id')
>pdata=pData(gse[[1]])[,columns]
>expression=exprs(gse[[1]])
>colnames(expression)=as.vector(pdata[colnames(expression),3])

But I feel confused, when I think about the way to handle with several GSMs
or user data.
applying getGEO function for GSM I have to use then Table(gse)$VALUE to
extract expression values and Meta(gse)$platform_id to know the GPL. I
understand how to do this easy when I have just 1 GSM. How should I manage
several GSMs?
from the start I supposed to use smth like this:

>gse=do.call("cbind",lapply('list_of_GSMs'),function(x) {
>getGEO(as.character(x),GSEMatrix=TRUE)
>}
but, thus, I get just expression values matrix, and I still don't know what
is the GPL and sample names.

Another idea (I did not check it yet, as I am not sure it is correct) is to
try to create an ExpressionSet (also for user data, after downloading them
through 'read.table'), but I also don't know how to create a phenoData file,
simply manually or there is a possibility to make it through the code.
having ExpressionSet I suppose I will can to use "pData" function like in
case of a GSE.
Doing all this I would like to be able to download and arrange the data in
the way, to use the rest of the functions which comes after 'gse=....' in
the up presented example.

Please, give me some hints at least at one of this points.

Thank's for you nice job.
Cheers

Alexei Levitchi
PhD in Genetics,
Bioinformatician at Laboratory of Bioinformatics
CBM, Area Science Park, Trieste, Italy
http://www.cbm.fvg.it/laboratories/bioinformatics_research

scientific researcher,
Center of Molecular Biology,
University of Academy of Sciences of Moldova
www.edu.asm.md



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