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

[Gordon K Smyth]

Dear Alper,

See the edgeR and GOseq Bioconductor packages, also the DEseq package. 
The edgeR package User's Guide gives a number of case studies:

http://www.bioconductor.org/packages/2.6/bioc/vignettes/edgeR/inst/doc/edgeR.pdf

Unfortunately, just treating RNA-seq as if it was microarray data will 
lose much of the benefit of the new platform.

Best wishes
Gordon

-----------------------------------------------
Associate Professor Gordon K Smyth,
NHMRC Senior Research Fellow,
Bioinformatics Division, 
Walter and Eliza Hall Institute of Medical Research, 
1G Royal Parade, Parkville, Vic 3052, Australia.
Tel: (03) 9345 2326, Fax (03) 9347 0852,
smyth at wehi.edu.au
http://www.wehi.edu.au
http://www.statsci.org/smyth

> Date: Sun, 2 May 2010 11:28:30 -0400
> From: Alper Yilmaz <alperyilmaz at gmail.com>
> To: bioc-sig-sequencing at r-project.org
> Subject: [Bioc-sig-seq] microarray to RNA-Seq
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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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