Hi,
I've just updated to DEXSeq 1.10.8. The manual claims that DEXSeq
fits a GLM for each gene (section 3.4 Testing for differential exon
usage), which I would expect. However, the formulae presented in that
section do not include any gene-level effects:
e.g., full model ~ sample + exon + condition:exon
In previous versions of DEXSeq incorporating the gene effect would
have been accomplished by selecting out the (exon) count rows
corresponding to a gene and performing the test individual on those
rows. i.e., with testGeneForDEU. But I don't see any similar partitioning
of the data by gene in DEXSeq 1.10.8. Can someone verify that it
is indeed fitting the GLM on a per-gene basis and how it is doing so?
I've just updated to DEXSeq 1.10.8. The manual claims that DEXSeq
fits a GLM for each gene (section 3.4 Testing for differential exon
usage), which I would expect. However, the formulae presented in that
section do not include any gene-level effects:
e.g., full model ~ sample + exon + condition:exon
In previous versions of DEXSeq incorporating the gene effect would
have been accomplished by selecting out the (exon) count rows
corresponding to a gene and performing the test individual on those
rows. i.e., with testGeneForDEU. But I don't see any similar partitioning
of the data by gene in DEXSeq 1.10.8. Can someone verify that it
is indeed fitting the GLM on a per-gene basis and how it is doing so?
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