Hi, I am analyzing expression data generated by microarray. An important step is mapping probes to gene symbols. My way to find the annotation(such as gene symbols) is to download the corresponding gpl files, which are often is very large and consume much time. Anyone has a better way to finish this work?
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Not really - using annotation files is the standard way of doing that step. If they're old / custom microarrays, it's also not a bad idea to blast the probes to the genome to make sure they still map where the annotation thinks they should map, but that increases, rather than decreases, the quantity of work involved.
Dear Jelena For GPL16977, I couldn't find the .annot file. Would you pleas help us? and, another question, How to find out the sequence of the probes? Regards.
sina.majidian, GPL16977 is the HuGene-1_1-st (Affymetrix Human Gene 1.1 ST Array). The annotation files can be downloaded from here: http://www.affymetrix.com/support/technical/byproduct.affx?product=HuGene-1_1-st-v1
There is also a Bioconductor package: Platform Design Info for Affymetrix HuGene-1_1-st-v1
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What type of microarrays are these? I'm mainly familiar with Affymetrix GeneChip arrays but I'm curious about the arrays you're using.