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

[Wolfgang Huber]

Dear Alper

this sort of clustering is an explorative data analysis technique, as 
such there is no single 'right' answer (although there are 'wrong' ones :)

So, what you suggest below is valid, although it could be suboptimal 
since the clustering could be dominated by few very large, but unprecise 
per-gene ratios especially when one of (Exp1-rpmk) or (Exp2-rpmk) is 
small. Section 4.6 and Fig.5 of this paper suggest a remedy: 
http://precedings.nature.com/documents/4282/version/2

	Best wishes
	Wolfgang




On 02/05/10 17:28, Alper Yilmaz 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
>
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber