Sorry, I forgot to include the URL for the tutorial that I'm referring to: http://manuals.bioinformatics.ucr.edu/home/R_BioCondManual#R_clustering
thanks, alper yilmaz On Sun, May 2, 2010 at 11:28 AM, Alper Yilmaz <[email protected]> wrote: > Hi, > > There's very nice tutorial about using Bioconductor to calculate > clusters (of genes) with different algoritms using microarray data. > > I would like to use the similar approach to calculate gene clusters > using RNA-Seq data. My question is, would it be okay to take the ratio > of RPMK values of Exp1 and Exp2 and use the natural log of that ratio > as if it's microarray data? > > Let's say Exp1 is control and Exp2 is treatment. I have RPMK value for > each gene for both samples. Then, ratio of Exp2(RPMK) over Exp1(RPMK) > is calculated and then natural log of that ratio is calculated. And > from here on, use the tutorial to calculate gene clusters. > > If log( Exp1-rpmk / Exp2-rpmk) is not a valid approach, what should I > do instead, so that I can use invaluable bioconductor tools that are > designed for microarray data mining, for RNA-Seq analysis? > > Regards, > > Alper Yilmaz > Post-doctoral Researcher > Plant Biotechnology Center > The Ohio State University > 1060 Carmack Rd > Columbus, OH 43210 > (614)688-4954 > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
