Entering edit mode
Alex Levitchi
▴
30
@alex-levitchi-4179
Last seen 10.3 years ago
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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