How to annotate GEO microarray datasets with GEOquery?

Question: How to annotate GEO microarray datasets with GEOquery?

4.4 years ago by

grayapply2009 • 240

United States

grayapply2009 • 240 wrote:

Hi, I read the GSE file into R as follows.

gse <- getGEO("GSE4928", GSEMatrix=TRUE)

Now I want to convert all probe IDs to gene symbols and write the entire annotated dataset back to my computer. What should I do? By the way, which dataset is stored in gse? SOFT formatted family file, MINiML formatted family file or Series Matrix File?

microarray annotation geo • 4.0k views

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modified 4.4 years ago by Sean Davis ♦ 26k • written 4.4 years ago by grayapply2009 • 240

4.4 years ago by

Sean Davis ♦ 26k

National Institutes of Health, Bethesda, MD

Sean Davis ♦ 26k wrote:

Take a look at this code:

gse = gse[[1]] # get just the first element in the list
head(fData(gse))
symbols = fData(gse)[,'Gene Symbol']

Now, you have the gene symbols. The gse object (after choosing the first element in the list using gse[[1]]) contains the information from the Series Matrix file AND the GPL file.

ADD COMMENT • link written 4.4 years ago by Sean Davis ♦ 26k

Thank you Sean. Now how can I export the Series Matrix file with the probes replaced by gene symbols?

ADD REPLY • link written 4.4 years ago by grayapply2009 • 240

After that, you can use:

expr_mat = exprs(gse)        # get the expression matrix
rownames(expr_mat) = symbols # Annotate the row names with gene symbols

ADD REPLY • link modified 4.4 years ago • written 4.4 years ago by Ce Gao • 10

Thank you, gaoce. That works perfectly. Where can I get the tutorial for this? The GEOquery document doesn't seem to have what you guys showed me above.

ADD REPLY • link written 4.4 years ago by grayapply2009 • 240

Unfortunately, this solution is not a general one due to the fact that not all GEO series have gene symbol or other annotation. What that means is that it is best to understand why the steps above work so that when you have another data set, you can follow the logic to come up with your own solution. That said, I am always interested in documentation improvements, so it you'd like to contribute, GEOquery is on github where I can accept pull requests.

ADD REPLY • link modified 4.4 years ago • written 4.4 years ago by Sean Davis ♦ 26k

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