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
