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n.lu
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@nlu-13144
Last seen 5.2 years ago
Hi,
I am quite new to this field. Does anybody have recomendations on the criteria to use for prefiltering genes in genefilter package? I have found a few of them (row SDS, IQR, intensity based filtering) but am not sure which one/what combination to use. Or should I not prefilter at all?
It depends on what kind of analysis it is you're doing.
My experiment has 4 groups - 2 different genotypes- wild type and a knockout - and then in both a group with disease and a control (WT control, WT disease, knockout disease, knockout control). I want to do analysis of differentaly expressed genes between these groups, and than add some pathway analysis when I have the list of DE genes to see if they belong to a certain bio process/pathway..
I don't think you'll need nonspecific filtering. I think you're better of using limma, it looks like a multi-factorial (two-way anova) design. Examples are in limma's user's guide for these kind of designs.
Thank you!
Why do you think that? "need" is a strong term, but filtering (or weighting, see my reply below) can improve an analysis by giving better power.