Hi,

I'm using DEXSeq and would like to do some filtering base on the minimum count number for each exon. With the default parameter, DEXSeq reports many significant events, many of which seem to have lower counts. Post from 1 or 2 years ago by Simon suggested that the minCount parameter in estimateDispersions() should be useful (https://support.bioconductor.org/p/45879/#45885). But I can't find it in current version of DEXSeq.

So what should I do to do the filtering? Thanks.

Best,

Jason

Hi Jason,

This parameter of the estimateDispersions function was deprecated, since now the independent filtering threshold is done automatically as described in the DESeq2 vignette. Note that the most recent versions of DEXSeq are internally using DESeq2.  

Alternatively, you can do some alternative filtering on low counts based on your own criteria and then correcting for multiple testing. For example, 

data("pasillaDEXSeqDataSet", package="pasilla")
dxr <- DEXSeq(dxd)
dxr$pvalue[rowSums( dxr$countData ) < 20] <- NA
dxr$padj <- p.adjust(dxr$pvalue, method="BH")

Best regards

Alejandro