...
Now lets take a look at the outliers of the first eigengene (patients 6 vs 367):
I guess it doesn't look too terrible. I also tried to remove all the listed variables as well as the first principal component and here is what I got in terms of the percent variance explained and the outliers: 
To me it looks worse than with the first principal component. Final: remove the batch, center, plate row and plate column from the data.