Hi,
I got 6 cel files from an Affymetrix microarray experiment: two conditions and 3 replicates of each condition.

I used the function plotDx from the R package AffyRNADegradation to review the rna degradation and this is what I got: 101053-01, 101053-02, 101053-03 are replicates of condition 1
101053-04, 101053-05, 101053-06, are replicates of condition 2
x axis shows the 11 different probes and y axis shows the average intensity over all genes.

This looks very different to the plot from the manual:

Now I don't know how to interpret my plot and what I have to do with the data. I'm very confused by the fact that even the order of the different samples is different in each probe. Also the intensity seems to be different depending on the probe.

Does anyone have an idea why the plot looks so strange? Would be very happy if someone could help :)