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]]

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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]