On Tue, Jul 6, 2010 at 9:31 AM, James W. MacDonald <jmacdon@med.umich.edu>wrote:

> Hi Jinyan Huang,
>
> On 7/6/2010 4:08 AM, Jinyan Huang wrote:
>
>> Does anyone have the exprience to use limma for two-color array:
>> GoldenGate Methylation Cancer Panel I (Golden Gate Cancer Panel
>> Methylation Illumina)
>>
>> I used it to analysis Methylation data for finding the different
>> methlated genes, but the result is not good. There are too many small
>> p-value the result. there are biology repeat in my data. My R code is
>> like this:
>>
>> library(limma)
>> exp<-read.table("exp.txt",F)
>> sample_id<-read.table("sample_id",F)
>> row.names(exp)<-exp[,1]
>> exp<-exp[,-1]
>> design<-read.table("design.txt",F)
>> explow<-exp[,design[1,]==-1]
>> exphigh<-exp[,design[1,]==1]
>> expsort<-cbind(explow,exphigh)
>> idlow<-sample_id[design[1,]==-1]
>> idhigh<-sample_id[design[1,]==1]
>> idsort<-c(idlow,idhigh)
>> colred<-rep("red",length(exphigh[1,]))
>> collow<-rep("blue",length(explow[1,]))
>> col<-c(collow,colred)
>> MA<-as.matrix(expsort)
>> exp_norm<-normalizeBetweenArrays(MA,method="scale")
>>
>
And this normalization is almost certainly not going to get you what you
want, assuming they are the "beta" values from Illumina.

Sean



> design_sort<-c(rep(-1,length(collow)),rep(1,length(colred)))
>>
>
> Wow. That's a lot of code to end up with a two-column matrix consisting of
> a column of -1s and a column of 1s. Is there some reason that modelMatrix()
> doesn't do what you want?
>
> I also suspect that the design matrix you came up with isn't correct for
> your experiment. I can't envision how the design matrix you have makes any
> sense. But without knowing the experimental design, I can't say for sure.
>
> I would recommend finding a local statistician who might be able to help
> you with this analysis.
>
> Best,
>
> Jim
>
>
>  fit<- lmFit(MA,design_sort)
>> fit<- eBayes(fit)
>> mylist<-topTable(fit,number=Inf,adjust="BH")
>>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
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