Hello,
Is anyone familiar with iClusterPlus?
I have been trying to use iClusterPlus to integrate methylation and expression data I have, but It's not clear to me what I might be doing wrong:
I am using beta values and RPKMS.
1) I filter out genes with low rpkm variability and probes (cpgs) with low beta value variability using kOverA function. 2) I use the tuning function to select the better results like:
set.seed(123)
for(k in 1:5){
cv.fit = tune.iClusterPlus(cpus=2,dt1=as.matrix(methx),dt2=as.matrix(exprx),
type=c("gaussian","poisson"),K=k,n.lambda=35,
scale.lambda=c(1,1,1),maxiter=20)
save(cv.fit, file=paste("cv.fit.k",k,".Rdata",sep=""))
}
3) My % of explained variation plot depending on the number of clusters is an increasing plot, (the more number of clusters, the most % explained variation), so maybe I should try more clusters than only 5, so I could see a better classification.
4) The clusters generated are shown in a heatmap: I can see the CpGs variation but for expression, the heatmap is almost everything the same color. Might this mean that I am filtering way too many genes?
I am using 17798 genes and 244 cpgs (maybe I need more cpgs)
How can I select the genes and probes belonging to each cluster? I can't seem to find the way by looking at the manual, everytime I get the same genes and probes.
Thank you so much.
