How to extract DEG from limmarResults object after beadarray analysis
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@d27aed9d
Last seen 17 hours ago
Germany

Hi,

I have followed the steps on analyzing a publicly available beadarray dataset and I ended up with a limmaResults object.

I'm familiar with DESeq2 and how to extract the results based on my conditions (e.g. Infected Vs Control), but I don't know how to do that with the limmaResults object. I looked in the Web, unsuccesfully. Any help is highly appreciated.

Thanks! Alex

beadarray limma • 156 views
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@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

I am the limma package author, but I don't know how to help you. The beadarray package has done a standard limma analysis but, instead of simply returning the limma object, all the results have been imbedded into a custom beadarray object of class limmaResults. It is unclear why that would be done as it cuts you out of all the downstream limma functionality. Anyway, there isn't much documentation for this class of object and it seems difficult to extract results from it --- you would need to be an S4 expert. The usual limma function topTable doesn't work on this object.

An alternative would be to run the limma functions directly instead of via the beadarray package, as I've suggested previously: beadarray error conversion