[BioC] report a potential bug in edgeR

[Gordon K Smyth]

Dear Shan Gao,

This is not a bug in edgeR.  Rather, your code contains a simple syntax 
error.

Looking at the help page for glmLRT would tell you that the third argument 
for glmLRT is 'coef' rather than 'contrast'.  If you want to enter a 
contrast, you need

   glmLRT(dge, glmfit.dge, contrast=aa[,"t0h-c0h"])

There are a number of examples in the edgeR documentation that show you 
this.

If you install edgeR 2.6.12, you will be also be able to use:

   glmLRT(dge, glmfit.dge, contrast=aa)

Best wishes
Gordon

--------------- original message ---------------
[BioC] report a potential bug in edgeR
wang peter wng.peter at gmail.com
Sun Aug 26 05:17:06 CEST 2012

> d <- DGEList(counts = d, lib.size = lib_size)
> #normalization
> dge <- calcNormFactors(d)
> rm(d)
>
> 
fac=factor(c('c0h','c0h','c0h','c24h','c24h','c24h','t0h','t0h','t0h','t6h','t6h','t6h','t6h','t12h','t12h','t12h','t12h','t18h','t18h','t18h','t18h',
+ 
't24h','t24h','t24h','t36h','t36h','t36h','t48h','t48h','t48h','c6h','c12h','c18h','c36h','c48h'))
> design = model.matrix(~fac)
> colnames(design) <- levels(fac)
>
> dge <- estimateGLMCommonDisp(dge, design)
> dge <- estimateGLMTagwiseDisp(dge, design)
> glmfit.dge <- glmFit(dge, design, dispersion=dge$tagwise.dispersion)
> aa = makeContrasts("t0h-c0h",levels=design)
> lrt.dgh <- glmLRT(dge, glmfit.dge, aa)

Error in coef.names[coef] :
   only 0's may be mixed with negative subscripts


> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936
[2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936
[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
[4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_People's Republic of China.936

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] edgeR_2.6.10 limma_3.12.1

loaded via a namespace (and not attached):
[1] tools_2.15.1

-- 
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute
Cornell University
Tower Road, Ithaca, NY 14853-1801
Office phone: 1-607-254-1267(day)
Official email:sg839 at cornell.edu
Facebook:http://www.facebook.com/profile.php?id=100001986532253

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