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How to obtain the probe density from GEO

I'm looking for the probe density of different array platforms to make a comparison. I have looked at the "platform" description given in the GEO webpage, the probe density isn't reported though.

I am a beginner in this field and I am not exactly sure about where to look for this information. Any help will be highly appreciated.

chip-seq gene
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updated by Calangoa • Calangoa • written by Natasha • Natasha

2 answers

I don't think there is a comprehensive, centralized database with this information. You will have to either search for each particular platform documentation, or download the data from GEO Platform and calculate the metrics of interest yourself.

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written by h.mon h.mon

Thanks a lot for the response. Could you please guide me to a reference to learn and understand how the probe density is calculated?

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written by Natasha • Natasha

do you mean you want the value of each gene? if so, you should go to GEO accession viewer of your GSE accession number of interest then click on data series for instance GSM12345 then it shows you a value of each gene.

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written by Calangoa • Calangoa

If my understanding is right, the value reported in GEO is the gene expression value that is given by a measure of the transcript array signal. Can we also obtain the probe density, for a gene, from GEO?

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written by Natasha • Natasha

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