Hi,

I wonder why for calculating gene lengths, they calculate the median of the transcripts in goseq manual? Its under section 5.3. I suppose it should be sum rather than median. The manual can be found here.

http://www.bioconductor.org/packages/release/bioc/vignettes/goseq/inst/doc/goseq.pdf

Cheers!
<p>The goal is to determine if there&#39;s a bias by gene length. In order to do this, one needs to derive some sort of gene length measure. There are a couple ways to do that:</p>

<ol>
	<li>Union gene model: The total non-redundant exonic length of a gene</li>
	<li>Estimated length: Derived from using expectation maximization, where you then have an estimate of the expected gene length within each sample</li>
	<li>Median transcript length: What&#39;s used here, which is just the median of the annotated transcript lengths.</li>
</ol>

<p>If you actually summed the transcripts, as you suggest, then you&#39;d get odd results for genes with many isoforms. The result also wouldn&#39;t match any biologically plausible length (e.g., if a gene has 20 isoforms, each ~1kb then your method would yield a length of 20kb rather than a more reasonable ~1kb estimate).</p>
