[BioC] Affymetrix quality control metrics with simpleaffy

Richard Friedman friedman at cancercenter.columbia.edu
Mon Oct 22 23:17:54 CEST 2007

Dear All,

	I  am using bioconductor 2.1 (R2.6) to do the affy quality  
assessment ratioes on
a set of 40 hgu133plus2 arrays. I have found that several of the  
parameters go outside the
ranges mentioned in the article by Bolstad et al i"Preprocessing high  
Density Oligonucleotide
arrays" in the book "Bioiioformatics and computational biology  
solutions using R and Bioconductor".

1. The average background values are supposed to be comparable to one  
The mean for the f0 slides is 65.6. the stdeve is 22.2. Only 2 slides  
are outside 2 stdevs of the mean.
one at 120 and the other at 134.

Should these slides be rejected on this basis?
What is a good criterion for an avbg to be different?

2. The scale factors are supposed to be withjin 3 fold of one another.
I have scale factors ranging from 0.386 to 3 with a median of about 1.
Shoudl I throwoout as many arrays as I need form the ends until the  
highest remaining scale factor
  is within a factor of 3 of the lowest remaining sclae factor. I  
would loose about 6/40 arrays like this.
Is this two stringent?
I owuld appreciate any sugegstions.

3. My minimum % present is 34.5 by maximum 49.5 and my median 45.0.  
Am I correct that I need not
through any arrays out on this basis.

4. All but a few of my actin3'5' and gapdh3'/5' ratioes are gretaer  
than 2. Does this pause a
serious problem?

The slopes are about the same and are alll within 2 standard  
deviations of the mean with the exception
of one point which is in 2.5 standard deviations of the mean.

Any guidance in this matter would be greatly appreciated.

Thanks and best wishes,
Richard A. Friedman, PhD
Biomedical Informatics Shared Resource
Department of Biomedical Informatics
Educational Coordinator
Center for Computational Biology and Bioinformatics
National Center for Multiscale Analysis of Genomic Networks
Box 95, Room 130BB or P&S 1-420C
Columbia University Medical Center
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)
friedman at cancercenter.columbia.edu

"The last 250 pages of the last Harry Potter
book took place in one day because alot
happened in that day. All of Ulysses takes
place in one day and nothing happened in that day."
-Rose Friedman, age 11

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