[BioC] Affymetrix Poly-A Controls

[Ann Hess]

I have some questions about Affymetrix Poly-A Controls.

The Affymetrix Data Analysis Fundamentals manual states that "Poly-A 
RNA controls can be used to monitor the entire target labeling 
process....All of the Poly-A controls should be called "Present" with 
increasing Signal values in the order of lys,phe,thr,dap."

I have some array data for which the Poly-A controls (lys, phe, thr, dap) 
are called Absent on many arrays.   In addition, the signal values 
consistently follow the order lys<phe<dap<thr across arrays.  To look at 
this, I took the average of all probe sets for each of the four controls 
and plotted these values by array.   I should note that the Hybridization 
Controls (bioB, bioC, bioD and cre) look good.  In addition, I verified 
that the GeneChip Poly-A RNA Control Kit was used.

Does anyone have experience with experiments where the Poly-A controls did 
not perform as expected?  What does this tell me about the data and the 
experimental protocol?  Should this have been checked by the core lab 
technician?

Any insight into this problem would be greatly appreciated!

Ann