[BioC] advise normalization for Agilent one color Microarray for mRNA and miRNA

[axel.klenk at actelion.com]

Dear Anke,

since I haven't seen a response to your post yet: I don't think there is
"the best" normalization method for either mRNA or miRNA but your
choice will rather depend on your data and assumptions... but have
a look at the BioC packages Agi4x44PreProcess and AgiMicroRna 
and their vignettes; they will let you try and compare some methods
easily. (Personally, I most often use vsn for mRNA and RMA for miRNA.)

Cheers,

 - axel


Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / 
Switzerland




From:
Anke Wendschlag <anke.wendschlag at googlemail.com>
To:
bioconductor at r-project.org
Date:
16.04.2011 12:29
Subject:
[BioC] advise normalization for Agilent one color Microarray for mRNA and 
miRNA
Sent by:
bioconductor-bounces at r-project.org



Dear Bioconductors,



I like to analyze Agilent one color Microarrays and need some input. Which
normalization method would be the best for mRNA and which for miRNA. 
Agilent
couldn’t get me a god support, because they have a specific for analyzing
data.



Thank you very much for your help!



Best,

Anke

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