[BioC] Correlation analysis of replicates

[Jenny Drnevich]

Hi Kai,

You can easily get correlation coefficients using R directly, but 
probably not AffylmGUI.

 >library(affy)

 >setwd("path_to_your_CELfiles")

 > rawdata <- ReadAffy() # this will read in all the CEL files in 
that directory

# to get correlation coefficients on raw, PM probe-level data between 
all pairs of arrays:
 >cor(pm(rawdata))

 >mas5data <- mas5(rawdata)

 >rmadata <- rma(rawdata)

# to get correlation coefficients using mas5 values or rma values 
between all pairs of arrays:
 > cor(exprs(mas5data))

 > cor(exprs(rmadata))

Don't forget that while the mas5 algorithm works independently on 
each array, the rma algorithm depends on which arrays are normalized together.

HTH,
Jenny


At 11:45 AM 11/11/2009, K Tre wrote:
>Hi Mark,
>
>Thanks for suggesting gene selector package, it might work. I am still
>wondering whether it's possible to upload just 2 Affymetrix chips in
>R/AffylmGUI and get a correlation coefficient rather than using Excel
>or something else. Does anybody know?
>
>Thanks,
>Kai
>
>On Thu, Nov 5, 2009 at 7:23 PM, Mark Cowley <m.cowley0 at gmail.com> wrote:
> >
> > Hi Kai,
> > i'm not sure about your first question, but...
> > re the correlation coefficient, take a look at the GeneSelector 
> package. In their original paper, they called  the correlation an 
> OrderScore if I recall correctly.
> > cheers,
> > Mark
> > -----------------------------------------------------
> > Mark Cowley, PhD
> >
> > Peter Wills Bioinformatics Centre
> > Garvan Institute of Medical Research, Sydney, Australia
> > -----------------------------------------------------
> >
> > On 06/11/2009, at 5:37 AM, K Tre wrote:
> >
> >> Hi,
> >>
> >> We are trying to compare affymetrix genelists generated a while back
> >> using MAS 5.0 to the new genelists generated using RMA analysis.
> >> Previously, we used to perform a comparison expression analysis of the
> >> replicates first (3 replicates for each condition) in order to 
> determine the
> >> false positive rate. Is there a way to do something similar in 
> RMA just for
> >> comparative purposes?
> >> Also, is it possible to compare only 2 chips at a time and generate a
> >> correlation coefficient? I checked the posting guide but couldn't find a
> >> previous email that would answer this question.
> >>
> >> Any help or pointing where to look is much appreciated,
> >> Thanks,
> >> Kai
> >>
> >>        [[alternative HTML version deleted]]
> >>
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>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
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e-mail: drnevich at illinois.edu