[BioC] Analyze Single Color Agilent Microarray Data

[axel.klenk at actelion.com]

Hi Srikanth,

you can of course try to read them into separate EList objects, filter 
those
for the common oligo subset (will depend on exactly what array type you
have), combine the subsets and continue with limma. 

This will get you around the purely technical problem of having different
array layouts BUT obviously not around the more serious problem of the
unfortunate study design that is confounding platform difference and
treatment effect...

Best,

 - axel


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




From:
"Srinivas M. Srikanth" <srikanth at ibioinformatics.org>
To:
<bioconductor at stat.math.ethz.ch>
Date:
03.08.2011 14:49
Subject:
[BioC] Analyze Single Color Agilent Microarray Data
Sent by:
bioconductor-bounces at r-project.org



Hi all,

I have data from single color agilent array exposed and unexposed to drug.
The exposed data is from 1x44 platform and unexposed from 4x44k. When i 
try
limma and load the files using read.maimages i get the error:

Error in RG[[a]][, i] <- obj[, columns[[a]]] :
  number of items to replace is not a multiple of replacement length

Please help me with this. How can load and perform analysis on this data.

Regards,
Srikanth

-- 
Srinivas M. Srikanth
Ph.D. Student
Institute of Bioinformatics
Discoverer, 7th Floor,
International Technology Park,
Bangalore, India
Mob:+917259692031

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