[BioC] Agilent and Limma

Tobias Straub tstraub at med.uni-muenchen.de
Wed Jul 22 09:15:36 CEST 2009

Hi Peter,

I am probably in a similar situation. I have just been convinced by an  
agilent rep to test their platform. So far we used Affy arrays. Now, I  
am absolutely willing to share experiences. However, I guess that  
these also depend a bit on on the detail of applications and organisms.

I am trying to do dual-color analysis comparing treated vs. untreated  
cells on 4x44 and we have Drosophila arrays. GeneSpring for whatever  
reason refuses to do proper analysis on dual color as far as i can  
see. So R/Bioconductor and manual processings seems to be the only way.

As Agi4x44PreProcess does not appreciate dual-color approaches, I did  
not test this package and don't know its status.

About absent/present calls: a simple solution would be to read the  
gIsPosAndSignif and/or rIsPosAndSignif column from your output files.

for the rest, my analysis is mainly based on limma. I do loess  
normalization within arrays and Aquantile between. A big question for  
me is how to treat multiple probes mapping to a single gene in case I  
want to summarize expression per gene. This appears not to be straight  
forward and is even more complicated in dual color approach.


On Jul 21, 2009, at 6:30 PM, Peter Robinson wrote:

> Dear conductors,
> we are currently trying to see if we can reproduce the results of  
> GeneSpring analysis using Bioconductor/limma and we are wondering  
> what the best interface is, i.e., at what point in the analysis to  
> input the Agilent data (image, raw, Gene-Spring-normalized), and how  
> to include the quality (present/absent) calls into the analysis. The  
> package Agi4x44PreProcess does not seem to be being actively  
> maintained (?). I wonder if anyone on this list would be willing to  
> share scripts/experiences on this.
> THanks Peter
> -- 
> Dr. med. Peter N. Robinson, MSc.
> Institut für Medizinische Genetik
> Universitätsklinikum Charite
> Humboldt-Universität
> Augustenburger Platz 1
> 13353 Berlin
> Germany
> voice: 49-30-450569124
> fax:   49-30-450569915
> email: peter.robinson at charite.de
> http://compbio.charite.de/
> http://www.human-phenotype-ontology.org
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Tobias Straub   ++4989218075439   Adolf-Butenandt-Institute, München D

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