[BioC] edgeR, comparing models

[Gordon K Smyth]

Dear Alpesh,

What you're doing looks correct.

However, if you are doing this analysis (Figure 2 from 
http://nar.oxfordjournals.org/content/40/10/4288 ) to decide whether you 
need to use tagwise dispersion for your data, note that we have never 
observed a real data set for which tagwise estimation is not required. 
Hence it seems unnecessary to make these plots as a routine diagnostic.

Yes, dispersion=0 is Poisson.

To plot highlighted blue points, see ?points as well as

   xy <- qqnorm(pcom)

etc.

Best wishes
Gordon

> Date: Mon, 21 May 2012 10:15:37 -0500
> From: Alpesh Querer <alpeshq at gmail.com>
> To: Bioconductor mailing list <bioconductor at r-project.org>
> Subject: [BioC] edgeR, comparing models
>
> Hello edgeR patrons,
>
> I have RNA-seq data for multiple samples with biological replicates, I want
> to look at the goodness of fit for
> fitting Poisson and NB models used by edgeR for common, trended and
> tag-wise dispersion. Does setting dispersion=0
> in glmFit use the Poisson model? Also I am using the following code to
> generate and compare qqplots for the models(figure 2 of
> the most recent edgeR manuscript),please let me know if I am using the
> appropriate method. Also how to plot the blue points (genes with poor fit)?
>
> y<-estimateGLMCommonDisp(y,design)
>
> fitcommon <- glmFit(y,design)
>
> y <- estimateGLMTrendedDisp(y,design)
>
> fittrended <- glmFit(y,design)
>
> y <- estimateGLMTagwiseDisp(y,design)
>
>
> fittagwise <- glmFit(y,design)
>
> gcom <- gof(fitcommon)
> gtren <- gof(fittrended)
> gtag <- gof(fittagwise)
>
> zcom <- zscoreGamma(gcom$gof.statistics,shape=gcom$df/2,scale=2)
> ztren <- zscoreGamma(gtren$gof.statistics,shape=gtren$df/2,scale=2)
> ztag <- zscoreGamma(gtag$gof.statistics,shape=gtag$df/2,scale=2)
>
>
> pcom=zcom[is.finite(zcom) ]
> ptren=ztren[is.finite(ztren) ]
> ptag=ztag[is.finite(ztag) ]
>
> par(mfrow=c(3,1))
>
> qqnorm(pcom)
> qqline(pcom)
>
> qqnorm(ptren)
> qqline(ptren)
>
> qqnorm(ptag)
> qqline(ptag)
>
>
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] edgeR_2.6.3         limma_3.12.0        BiocInstaller_1.4.4
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.0
>
>
> Thanks,
> Al

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