[BioC] Agilent and Limma

Francois Pepin fpepin at cs.mcgill.ca
Tue Jul 21 19:46:21 CEST 2009

Hi Peter,

Are you trying to just replicate the results exactly or you want to try 
another set of analysis method?

It should be possible to replicate most of the results from GeneSpring 
using Bioconductor, although GeneSpring is not very good at describing 
all their methods (but maybe it's changed since). Unless you want to 
better understand the GeneSpring procedure (or if you don't trust their 
results), this maybe not what you want to do.

If you want to try another analysis technique, then there is a whole 
world in front of you, both for the normalization and for the 
differential expression. If you just want to see what limma tells you, 
then you might just want to use the normalized values from GeneSpring, 
otherwise I would start from the raw values. Either way, I wouldn't 
start from the image level

The Agilent scanner (if that's what you're using), can assign weights to 
each spot, which limma can use. I personally am not a big fan of 
present/absent calling methods, so maybe someone who use them more can 
chime in.

The best advice is probably to read the limma user guide. you should see 
pretty much all the information that you need to get started (including 



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

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