Hi Jim, On 12/03/2010 02:05 PM, Jim Silverton wrote:
Hello, I want to simulate some RNA seq data and use fisher's exact test. Is there code available for this?
There is a simple/naive/non-realistic example of how to simulate reads (not RNA-seq specific) in the man page of BSgenome::getSeq() function. See ?getSeq, then look for the "D. EXTRACTING A HIGH NUMBER OF RANDOM 40-MERS FROM A GENOME" example. Just a starting point. To be more realistic the code would need to be adapted to reflect the protocol used and integrate experimental errors. Doesn't sound like a simple task but maybe someone on the list already tried to do something like this?
Secondly do you have the code for Tarone's Test and Gilbert's discrete FDR?
Someone else will know... Cheers, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: [email protected] Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
