Question: Filtering during RNA Seq analysis?
gravatar for aggregatibacter
2.2 years ago by
Bonn, Germany
aggregatibacter90 wrote:


I have roughly 100 samples (2 groups) of noisy human tissue data. Thinking about filtering to improve the multiple testing situation. Thus far, I filter by cpm values (calculated using edgeR after counting with featurecounts), and run voom/limma afterwards. I have also stumbled over htsfilter, and thought about variance filtering.

Now I heard that filtering, at least by variance or htsfilter, was per se incompatible with limma or other empirial Bayes methods.

What do you experts think/suggest?

Many thanks!

rna-seq • 1.1k views
ADD COMMENTlink modified 2.2 years ago by i.sudbery2.7k • written 2.2 years ago by aggregatibacter90
gravatar for i.sudbery
2.2 years ago by
Sheffield, UK
i.sudbery2.7k wrote:

You might also try "Independent Hypothesis Weighting" as implemented in the IHW Bioconductor package and described it this paper:

Instead of filtering genes to conserve power, it weights them. It is compatible at least with DESeq2 and is used in their vignette (i suspect it can be used in conjunction with other packages as well).

ADD COMMENTlink written 2.2 years ago by i.sudbery2.7k
gravatar for Devon Ryan
2.2 years ago by
Devon Ryan86k
Freiburg, Germany
Devon Ryan86k wrote:

The package you're looking for is genefilter. As an aside, that's used automatically by DESeq2.

BTW, filtering by variance isn't compatible with any RNAseq package that I'm aware of (variance is convoluted with the DE test).

ADD COMMENTlink written 2.2 years ago by Devon Ryan86k

Thanks guys for your suggestions. I will definitely also try DESeq2. I have the feeling that it is quite en vogue at the moment, is that correct? Thus far, I primarily use limma, because I was brought up with arrays, and usually need to correct for random and fixed factors.

ADD REPLYlink written 2.2 years ago by aggregatibacter90
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