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Question: Nonspecific filtering of microarray data
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gravatar for n.lu
5 months ago by
n.lu0
n.lu0 wrote:

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?

 

 

ADD COMMENTlink modified 5 months ago by Wolfgang Huber13k • written 5 months ago by n.lu0

It depends on what kind of analysis it is you're doing.

ADD REPLYlink written 5 months ago by b.nota290

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..

ADD REPLYlink written 5 months ago by n.lu0

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.

ADD REPLYlink written 5 months ago by b.nota290

Thank you!  

ADD REPLYlink written 5 months ago by n.lu0

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.

ADD REPLYlink written 5 months ago by Wolfgang Huber13k
1
gravatar for Wolfgang Huber
5 months ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:

In many cases, using data-driven weights for the multiple testing computation is a better approach than yes/no filtering, see e.g. the IHW vignette and the associated paper. The vignette also gives hints on the choice of the weighting covariate and diagnostic plots.


 

ADD COMMENTlink written 5 months ago by Wolfgang Huber13k
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