Rna Degradation Plot Of Transcript Arrays

Question

[Assa Yeroslaviz]

Hi everyone,

We are working on the affymetrix transcript arrays (HuGene-1_0-st-v1). As a first step I ran a quality control check. One of the steps was the RNA degradation plot.

As I know it from the other Oligonucleotide arrays, in the best case scenario the mean intensity is low at the 5' end and gets higher towards the 3' end. What I got in this analysis was a different picture: RNADegplot

Here it goes higher and in the middle down again. Is this behaviour a normal situation for transcript arrays?

Can someone point me to a paper or an explanation for this behaviour?

Thanks a lot

Assa