[BioC] Normalization of Affymetrix microarray data with spike-in hybridization controls?

[Steve Lianoglou]

... and ... re: spike ins:

On Fri, Nov 9, 2012 at 10:02 AM, James W. MacDonald <jmacdon at uw.edu> wrote:
[snip]
> So it isn't unheard of to do what you suggest. However, this is ground that
> was worked over fairly thoroughly in the middle of the last decade, and
> except in fairly pathological cases (e.g., when a preponderance of genes are
> differentially expressed), a simple quantile normalization seems to work
> pretty well, and has since become more or less the paradigm.

here's another example:

Revisiting Global Gene Expression Analysis
http://www.sciencedirect.com/science/article/pii/S0092867412012263

It's another pathological case -- not exactly the one you suggest, but
this was from recent work showing that Myc is something like a rising
tide that lifts all boater -erm -- I mean, genes.

Transcriptional Amplification in Tumor Cells with Elevated c-Myc
http://www.sciencedirect.com/science/article/pii/S0092867412010574

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact