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Filtering input data

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Filtering input data
2/16/07 1:28 PM
Hello MapMan group,

Does anybody have an opinion about filtering expression data on flags prior to import into MapMan? I use limma for determining differential gene expression (DE) as well as list generation for MapMan input. For DE analysis, I filter out poor (flagged) spots prior to fitting my models. Thus, the resulting M values, and eventual MapMan input, differs based on filtering or not filtering. Subsequently, my MapMan output also differs, although slightly, based on this fitltering decision.

I assume the answer would be determined on a case-by-case senerio, but I am interested in what others are doing. Thanks again for the great software- dave

Re: Filtering input data
2/16/07 1:42 PM as a reply to Dear 7wd.
Dear Dave,

I would suggest you read up a bit on the bioC mailing list about filtering based on spots. I would suggest using spot weights to down-weigh flagged spots in limma instead of filtering them out completely. I think Gordon Smyth made one or two comments about that.

Reagrdless, you should get similar results in the end hopefully, if the response was consistent.

I however shy spotted arrays as much as possible....