Table expression data from GEO file
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lsbew • 0
@lsbew-23269
Last seen 2.1 years ago

Hi everybody,

I downloaded a GEO dataset with GEOquery and have my gse file turned into an ExpressionSet. I have two questions how to further proceed.

1) How can I get a table with all the gene expression levels?

2) How can I compare the Row labeling to the gene information from the CHIP that was used for the Assay? I know that there is a package for the CHIP infos that I need but I have no idea how to assign the gene names to the IDs.

I am not very familiar with R, so please excuse that my questions might be confusing.

GEO expression GEOquery • 318 views
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Robert Castelo ★ 2.9k
@rcastelo
Last seen 1 day ago
Barcelona/Universitat Pompeu Fabra

hi,

1) the function exprs(eset), where eset is an ExpressionSet object, will give you a matrix of the expression values stored in the object, with rows corresponding to features and columns to samples.

2) I guess you mean how to get gene symbols from microarray chip feature identifiers. Assuming your ExpressionSet object is called eset, you can use the function getSYMBOL() from the annotate package:

syms <- annotate::getSYMBOL(featureNames(eset), annotation(eset))


If you are unfamiliar with R, and probably then with this support site, I strongly recommend you to read the Bioconductor posting guide to learn how to get the best answers in this support forum.

cheers,

robert.