please keep things on list

since your log.ratios are on the log base 2 scale, calculating fold  
change is a case of simple subtraction, followed by unlogging.

logfc.1vs2 <- log.ratio[,2] - log.ratio[,1]
fc.1vs2 <- 2^logfc.1vs2

repeat this for your comparisons of interest

cheers,
Mark

On 31/08/2010, at 12:53 PM, ashwin Vishnuvardhana wrote:

> Hi Mark,
> I dont have any replicate samples I just have one sample per  
> experiment. and basically do we need to use log ratio data i.e.
> log.ratio <- MA$M using this code. from Dr. Peder code.
>
> Thanks
> Ashwin
>
> On Mon, Aug 30, 2010 at 6:06 PM, Mark Cowley  
> <m.cowley@garvan.org.au> wrote:
> 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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