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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