[BioC] RNA degradation plot of transcript arrays

[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 (see attachment).

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
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