[BioC] Limma for GoldenGate Methylation Cancer Panel I

[James W. MacDonald]

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")
> 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")
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues