The chips were run in two different days one month apart. first 24 samples and then the other 24 samples.
The negative controls of the second batch have a wider range.
And wen looking at the MDS and PCA we can see that the main parameter for grouping samples is the run day (the two chips starting with 835... where done the same day and the other two another day)
I have used the nice rnbeads R package for reporting the batch effects.
Now I am exploring two methods of correcting the batch effect:
- limma using the batch date as block effect
- design <- model.matrix(~Block+Treatment)