[BioC] Affymetrix Poly-A Controls

[James W. MacDonald]

Hi Ann,

Ann Hess wrote:
> 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?

I don't use mas5 numbers, and don't much believe in the utility of the 
P/M/A calls, so cannot comment on whether or not these controls are 
usually called present. However, when I have looked at these controls, I 
pretty much always see the same pattern that you mention, although the 
dap control expression value can vary from dap<lys<phe<thr to 
lys<phe<dap<thr.

I am not so sure these controls are that useful, and I would personally 
look at other measures of quality to assure myself that the data were of 
reasonable quality.

Best,

Jim


> 
> Any insight into this problem would be greatly appreciated!
> 
> Ann
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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