[BioC] urgent help: meet an error in using edgeR

[wang peter]

HELLO all: hope some one can help me on such error.

> 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)#估计tag wise方差，必须先估计common方差
> dge <- estimateGLMTagwiseDisp(dge, design)
> glmfit.dge <- glmFit(dge, design, dispersion=dge$tagwise.dispersion)#注意推荐使用tag wise方差
> t0_c0 = makeContrasts("t0h-c0h",levels=design)
> lrt.dge <- glmLRT(dge, glmfit.dge, contrast = t0_c0)
> result <- topTags(lrt.dge, n=dim(dge)[1], adjust.method="BH", sort.by="p.value")


Error in abs(object$table$logFC) :
  Non-numeric argument to mathematical function

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
-- 
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute
Cornell University
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