hi Lucia,


On Tue, Apr 23, 2013 at 9:03 PM, Lucia Peixoto <luciap@iscb.org> wrote:

>
>
> I am thinking about transforming my RNAseq data, but a lot of the genes
> have very low counts. Won't either rlog or voom transformation require the
> counts to be high to be valid?
> Should I filter low count instances before doing the transformation and the
> PCA? how low is too low for ti to work?
>


You probably don't have to worry about counts being too low for the
transformations to work. Here, 'work' meaning accounting for differences in
scale between the sample (sequencing depth) and the mean-variance
relationship typical of count data.

There is such a thing as too low for subsequent differential analysis, just
as with microarrays when the signal lies below the noise. You can see this
with an MA-plot, for a data set with some true DE genes, the genes with low
counts are less likely to have significant p-values.

Mike

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