[BioC] Calculating fold change (RG.MA in limma )

[Mark Cowley]

hi Ashwin,
how many replicates per condition do you have?
If you have more than one, then take a look at chapter 7 in the limma  
users guide. This will help you get fold change, and p-values for your  
comparisons of interest.
Fitting an appropriate linear model on the log.ratio matrix will  
average the replicates, then fitting appropriate contrasts will get  
you the difference between each of your conditions.

library(limma)
limmaUsersGuide()

hope that helps

cheers,
Mark


On 31/08/2010, at 5:03 AM, ashwin Vishnuvardhana wrote:

> Hi,
> I am currently working on two channel exiqon data analysis work and  
> I have
> questions about calcualting fold change values after normalized data.
> I am  using R lima package and folowing Dr.  Peder Worning code(
> https://stat.ethz.ch/pipermail/bioconductor/2009-March/026738.html)*
> RG.MAin limma
> * for getting the outputs and the code is working is excellent. But my
> question is
> after getting ouptut of *Cy.norm, cy.5 norm and log.ratio I want to
> calculate fold change among samples as my experiments has 3 samples  
> and I
> want to see up and down regulated genes among sample 1 vs sample 2 ,*
> *sample 1 vs sample 3. So which data should i need to use ??*
> *is logratio data or cy3 and cy.norm data.*
> **
> *Any help is greatly appreciated*
> Thanks
> Ashwin
>
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