[BioC] Agilent and Limma
tstraub at med.uni-muenchen.de
Wed Jul 22 09:15:36 CEST 2009
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
> Augustenburger Platz 1
> 13353 Berlin
> voice: 49-30-450569124
> fax: 49-30-450569915
> email: peter.robinson at charite.de
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Tobias Straub ++4989218075439 Adolf-Butenandt-Institute, München D
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