Could you tell us more information? Which array are you using? How
probes have the probeset?
I have seen these plots in the past with the Rat Genome U34 Set.
The idea of the Affy deg plots is that all the arrays have a similar
behaviour, as in your case. So I would take as acceptable your arrays.
Hospital Clinic (Barcelona, Spain)
>Degradation plots that I have done in the past have usually
>produced plots that increase towards the 3' end in a roughly
>uniform manner. I have done this (breast) experiment on a new
>chip which results in the folowing plot:
>This seem to be rather strange,as it peaks in intensity before
>the farthest 3' end. Is there any explanation for this or is there
>any documetnation of this happening elsewhere?