[Bioc-sig-seq] microarray to RNA-Seq

[Alper Yilmaz]

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 <alperyilmaz at gmail.com> 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
>