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

	[[alternative HTML version deleted]]

