I am currently trying to run WGCNA for my microarray dataset. I have run QC checks and removed outliers, then I have normalised using rma() and finally when I run the code to make a sample tree I had 1 outlier. I then removed that outlier manually and run the code from the start with the samples without the outlier sample. However when I go to make the sample tree again there is always another outlier. What is happening?
I am up to the hclust() step in the WGCNA data input tutorial.