I study on RNA-seq expression dataset about one cancer in TCGA. I downloaded FPKM dataset and removed batch effect by ComBat() function. Now, I used
pvclust for clustering 72 samples and the result of that can access in this link.my code for running pvclust is as below:
fit_LMS <-pvclust(datForpvclust,method.hclust = "average", method.dist = "euclidean",nboot=10000, parallel=TRUE ) pvrect(fit_LMS, alpha=0.95)
As you see, by alpha=0.95 just 3 clusters are significant although in right cluster a few clusters have been included. really I can't analysis this result.
So, I have 2 questions:
1- What is the interpretation of
pvclust dendrogram? Does my dataset has meaning full clusters?
2- I am interested in the height of tree cut in the dendrogram, which height is better for this dataset based on pvclust result? H=105 or H=110 or another height?
I appreciate it if anybody shares his/her comment with me.