A friend of mine was interested in selecting stable genes from RNA-Seq experiment, stable meaning genes with expression not affected by changing conditions.
I think the easiest solution is using partitioning function implemented in cummeRbund (K-means clustering):
ic<-csCluster(myGenes,k=4) head(ic$cluster) icp<-csClusterPlot(ic) icp
Of course, it’s good to play with `k` value, so you indeed get some cluster with genes that are of interest.
Then, once you have some candidates, you may want to look for genes having similar expression patterns.
mySimilar<-findSimilar(cuff,"my_gene_name",n=20) mySimilar.expression<-expressionPlot(mySimilar,logMode=T,showErrorbars=F) mySimilar.expression