Filtering out lowly expressed genes on Affymetrix Gene ST arrays
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knaxerova ▴ 10
@knaxerova-7541
Last seen 5 months ago
United States

Hi all,

the limma user guide suggests filtering out probe sets that are not or barely expressed across conditions. In past analyses, I have simply handed all "main" probe sets over to limma, but I think it might be interesting to play around with different filtering approaches to increase power. I have found some very good posts discussing this question (e.g. https://support.bioconductor.org/p/57753/), but I would be interested to hear about people's filter habits & opinions: do you usually achieve best results with aggressive filtering, or is it better to be gentle? I know this may very much depend on the data in question... but I am still curious about the experience of others.

Many thanks in advance.

Kamila

Affymetrix Gene ST limma • 853 views
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This doesn't answer your question directly, but you might consider trying the UPC function in the SCAN.UPC. It doesn't use the control probes (for algorithmic reasons), but it identifies genes that are turned "on" or "off" and can be applied to the ST arrays. One use of this tool is to filter out lowly expressed ("off") genes.

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