Hi Diya. Just to add my 2 cents to this, although Mathieu has pretty much covered it.
There are no online tutorials (that I know of) for exactly what you want to do, but your proposed analysis is very standard. lmFit() of limma can work directly on your matrix of logged data. Consult the limma documentation (e.g. the limma user's guide) on how to do this. Cheers, Mark On 29-Aug-09, at 12:13 AM, Diya v wrote: > Hi > > I have 2 control and 2 treatment groups of MoGene-1_0-st.I have the > data normalized and and a data matrix after fit(plm) is performed. > > I want to do statistical analysis for differentially expressed ganes. > > Can I take the datamatrix generated from aroma.affymetrix and do the > analysis with limma > > Is there any online tutorial for this? > > Thanks, > Diya > > --- On Fri, 28/8/09, Mathieu Parent <parent.math...@gmail.com> wrote: > > From: Mathieu Parent <parent.math...@gmail.com> > Subject: [aroma.affymetrix] Re: Discussion on gene-1-0-st-array- > analysis > To: aroma-affymetrix@googlegroups.com > Date: Friday, 28 August, 2009, 5:58 PM > > Hi, > > They way it has been proposed to me, is to extract the matrix from > the normalised and summarised data, log it and pass into the LIMMA > package for differential expression analysis. > > What is your experimental design ? > > Math > McGill University > > On Thu, Aug 27, 2009 at 3:46 PM, Diya Vaka <biotechd...@gmail.com> > wrote: > > Hello All, > > I want to know about the up and down regulated genes.So how am i > supposed to proceed after this step > > Diya > > > > > > > Love Cricket? Check out live scores, photos, video highlights and > more. Click here > > > ------------------------------ Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robin...@garvan.org.au e: mrobin...@wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 ------------------------------ --~--~---------~--~----~------------~-------~--~----~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
