[BioC] Re : Analysis of differentially regulated genes

[phguardiol at aol.com]

Dear all,

I m not sure about what kind of normalization process can be used for 
methylation status analysis because of the potential distribution of 
these data...
I would be curious to know what people from this group think about this 
point and if it could explain part of these results below...
Thanks

Philippe Guardiola

-----E-mail d'origine-----
De : r.kandimalla <r.kandimalla at erasmusmc.nl>
A : bioconductor at stat.math.ethz.ch
Envoyé le : Lundi, 10 Novembre 2008 16:42
Sujet : Re: [BioC] Analysis of differentially regulated genes






Dear all, 
 

I would like to here your comments and suggestions regarding my 
analysis
described below. 

Im working with genomewide screening of CpG methylation with agilent 
two
color CpG arrays with a common reference design. 

I have got the data of the future extraction and did loess
normalisation, applied limma to check for the differentially regulated
genes. In one of the comparision i have superficial and invasive 
tumors, 

surprisingly i saw zero differentially regulated genes which is quiet
unrealistic. 

Here is the R session: 

 >
design1<-cbind(SM=c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0
,0,0,0,0,0,0,0),
I=c(0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1))
 

 > colnames(design1)<- c("SM", "I") 

 > design1 

 > dim(dataset1) 

[1] 237220     34 

 > fit<- lmFit(dataset1, design1) 

 > ngenes <- nrow (dataset1) 

 > cont.matrix<- makeContrasts(SMvsI=SM-I, levels=design1) 

 > cont.matrix 

      Contrasts 

Levels SMvsI 

    SM     1 

    I     -1 

 > fit2<-contrasts.fit(fit, cont.matrix) 

 > fit2 <-eBayes(fit2) 

 > topTable(fit2, adjust="fdr") 

 > SMvsI <- topTable(fit2, number=ngenes, adjust="fdr") 

 > results <- decideTests(fit2,adjust.method="fdr",p.value=0.05) 

 > summary(results) 

    SMvsI 

-1      0 

0  237202 

1       0 
 

Best regards, 
 

--
Raju Kandimalla, PhD student 

Erasmus MC 

Department of Pathology 

JNI,Room H Be-302 

Dr. Molewaterplein 50 

3015 GE Rotterdam-NL 

phone: +3110-7043093 

fax: +3110-7044762 

r.kandimalla at erasmusmc.nl 

http://www.erasmusmc.nl/pathologie 
 

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