Question: How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
2
gravatar for gabriel.rosser
7 months ago by
gabriel.rosser90 wrote:

McCarthy, D.J., Chen, Y., and Smyth, G.K. (2012). Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res 40, 4288–4297.

https://academic.oup.com/nar/article/40/10/4288/2411520/Differential-expression-analysis-of-multifactor

In Figure 2 of this paper, the authors show that estimating dispersion on a per-gene basis is more compatible with their data:

Figure 2 of edgeR paper

(I realise I'm probably not supposed to copy the figure here, but it's an open access paper and I've acknowledged the source)

I think understand broadly what is being demonstrated here (please correct me if I'm mistaken): When we estimate dispersions, that is an implicit model of the ratio of the mean to the standard deviation of each gene. Here, the authors are showing, with QQ plots, that the per-gene model describes the observed ratio better than a common dispersion value. Each dot in the plot corresponds to a gene.

I'd like to generate this figure for my own data, but I don't understand how to compute the two vectors required as inputs to qqplot(). I'm guessing that one might be the log likelihood after fitting the GLM?

Thanks for any light you can shed (code also gratefully appreciated, but no obligation)

ADD COMMENTlink modified 7 months ago • written 7 months ago by gabriel.rosser90
1

If you want an answer from the authors themselves, you should ask this question on the bioconductor support site. Usually Gordon Smyth replies within a day.

https://support.bioconductor.org/t/Latest/

ADD REPLYlink written 7 months ago by b.nota3.6k

OK, thanks for pointing that out! If I get a reply (and understand it), I'll answer my own question.

ADD REPLYlink written 7 months ago by gabriel.rosser90
3
gravatar for gabriel.rosser
7 months ago by
gabriel.rosser90 wrote:

I followed b.nota's suggestion and asked on the Bioconductor support site. I got a fairly detailed response from Gordon and Davis. See the full discussion here: https://support.bioconductor.org/p/94310/

TL;DR

There's a gof() function included in edgeR that should do exactly what I needed.

ADD COMMENTlink written 7 months ago by gabriel.rosser90

glad to see the OP answering their own question.

ADD REPLYlink written 7 months ago by vchris_ngs4.1k

Thanks. I feel a bit arrogant marking it as the accepted answer - is that reasonable etiquette?

ADD REPLYlink written 7 months ago by gabriel.rosser90
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