How to create gene level data from a probe level data?
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17 months ago

Hi,

I have a probe level data with me and would like to create a gene level analysis. Suppose an array has 10 different probe sets corresponding to the same gene. In practice, what is the suitable method to assign multiple probes to a gene? Does summarizing across the 10 probes to come up with one value at the gene level or averaging by arithmetic mean over the probes to gene assignment?

Thank you,

Toufiq

R sum mean gene microarray • 714 views
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Hamid Ghaedi, thank you very much.

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I am not sure if this is "best practice" but, generally, I have been keeping all duplicate genes, and just using a function such as make.unique() to add a .# to every duplicate so for example YFG.1, YFG.2, YFG.3, ...

This way all data is kept, and, just in case, no interesting data is lost!

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Pratik Mehta, thank you for the prompt response. But, after the probe to gene mapping, using this gene level matrix I would be mapping/merging to another third party gene annotation database. In case, If I use make.unique () then the genes renamed by a suffix (for instance YFG.1, YFG.2, YFG.3, ...) will be lost during the mapping process since the third party database would only contain gene (YFG, but not YFG.1 or YFG.2 etc). So it is important for me to include a summarized gene or averaged gene while mapping.