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.pdfUnfortunately, 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, [email protected] http://www.wehi.edu.au http://www.statsci.org/smyth
Date: Sun, 2 May 2010 11:28:30 -0400 From: Alper Yilmaz <[email protected]> To: [email protected] 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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