[BioC] spiked controls wrong order on samples wit 2 rounds of amplification normalize with GCRMA

[Richard Friedman]

Dear Bioconductor list,

	 "Design and Analysis of DNA Microarray Investigations"
by R. Simons et al. p. 50 states that the Affymetrix spike-in signals  
should
be in the order

BioB < BioC < BioD < Cre.

I have normalized 38 mouse 430 2.0 arrays with GCRMA 1.10
in Bioconductor 2.0
(I am using the older GCRMA/Bioconductor until I understand the  
current version better
and am sure it is an improvement). The RNA was prepared by
2 rounds of amplification.

Most of the arrays follow the above order of spike-in signals:

But 3 don't, the worst of which is:


AFFX-BioB-3_at     2.294069074
AFFX-BioC-3_at     3.3599997
AFFX-BioDn-3_at     8.462104429
AFFX-CreX-3_at     11.09629022

AFFX-BioB-5_at     3.322136446
AFFX-BioC-5_at     3.093697367
AFFX-BioDn-5_at     8.079313416
AFFX-CreX-5_at     11.06766875


Is the decrease rather than increase between FFX-BioB-5_at
and AFFX-BioC-5_at a cause to discard the array.

All of the regular affy quality checks, plus the RNA degradation  
plot  and
the AffyPLM NUSE ,RLE, and signed  residual image for this chip  
looked fine.

THANKS!
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
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
http://cancercenter.columbia.edu/~friedman/

"I like it how they tell us that something can either be rational or  
radical-and this is
a college." -Isaac Friedman, age 18