[BioC] how to design comparision using edgeR

[James W. MacDonald]

Hi Shan Gao,

On 7/18/2012 10:34 AM, wang peter wrote:
> dear all:
>
> my data is composed of 35 samples, have two factor
> time and treatment
>
> i want to find DE genes between 6h and 0h due to the treatment
> effect,removing the time factor effect.
I am not sure what you mean. How can you find DE genes between two times 
after removing the time factor effect?

The default of

glmLRT(dge, glmfit.dge)

will give you the treatment vs control comparison, adjusted for time.

>
> how can i use glamLRT to do test
>
> raw.data<- read.table("expression-table.txt",row.names=1)
> lib_size<- read.table("lib_size.txt");
> lib_size<- unlist(lib_size)
> d<- DGEList(counts = raw.data, lib.size = lib_size)
> dge<- d[rowSums(d$counts)>= length(lib_size)/2,]
>
> #normalization
> dge<- calcNormFactors(dge)
>
> treatment=factor(c(rep('control',6),rep('treated',24),rep('control',5)))
> time=factor(c('0h','0h','0h','24h','24h','24h','0h','0h','0h','6h','6h','6h','6h','12h','12h','12h','12h','18h','18h','18h','18h',
>               '24h','24h','24h','36h','36h','36h','48h','48h','48h','6h','12h','18h','36h','48h'))
> design<- model.matrix(~time+treatment)
>
> dge<- estimateGLMCommonDisp(dge, design)
> dge<- estimateGLMTagwiseDisp(dge, design)
> glmfit.dge<- glmFit(dge, design,dispersion=dge$common.dispersion)
>
> lrt.dge<- glmLRT(dge, glmfit.dge, coef=2)??????????????????????????????
This will give you the 12hr - 0 hr comparison, adjusted for treatment 
status.

Best,

Jim


>
>
>
> how can i use glamLRT to do test
>
> --
> shan gao
> Room 231(Dr.Fei lab)
> Boyce Thompson Institute
> Cornell University
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>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099