[BioC] One-color spotted microarrays analysis

Wolfgang Huber huber at ebi.ac.uk
Wed May 27 00:15:08 CEST 2009

Pier-Luc Poulin ha scritto:
> Hi everyone,
> I have a general question about microarray data analysis using bioconductor.
> We are using a 32k custom spotted oligo array and we are planning on doing one-color microarray experiments. We need advice on how to proceed with data normalization and analysis. We have searched in the literature and in the vignettes and user guides of BioConductor but it seems that almost every experiment with spotted arrays is done with two colors. No documentation exists for single channel spotted microarrays, except for the article by 't Hoen et al., 2004, Nucleic Acids Research.
> Does anyone have knowledge or suggestions on methods or Bioconductor packages that could be used for this kind of analysis?
> Thanks, 
> P-L Poulin
> Research assistant
> Université Laval
> www.arborea.ca
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Dear Pier-Luc

from the data analysis point of view, it does not make a substantial 
difference whether the DNA on the array probes was brought there by a 
spotter or synthesized in situ.

There is an enormous amount of documentation on the analysis of 
one-colour arrays, and chapter 7.2 of the limma vignette might be a good 

More specifically, you could consider the justvsn function from the vsn 
package or the normalizeQuantiles function from the limma package for 
normalisation; and the arrayQualityMetrics package for quality-related 

Best wishes

Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber

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