[BioC] Re: random location of duplicate spots and use of limma

[Saroj Mohapatra]

From: "Ingunn Berget" <ingunn.berget at umb.no>

I thought that the methods giving the highest correlation would be best
for further analyses, but the highest correlation was obtained with no
background correction and no normalisation. I found this very strange
since the background is not uniform within the arrays, and all
litterature says that microarray data should be normalised.

Ingunn

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Ingunn:


Please check the intensity-level of the spots. If they are mostly low
(that is spot-intensity is close to background-intensity), then
background-correction would introduce greater variability among
spot-replicates.

Something of this sort is reported by Speed'S group in the context of
microarray image analysis. 

Yang et al (2000) Comparison of methods for image analysis on cDNA
microarray data. Technical report # 584,Nov 2000.




------
Saroj K Mohapatra, MD
Research Associate
Wayne State University School of Medicine
110 E Warren Avenue, # 311
Detroit MI 48201

saroj at wayne.edu