Re: [R] [BioC] similarity between two gene lists with varied length

The made4 package in bioconductor can report gene list similarities. --- Deanne Taylor PhD Executive Director, Bioinformatics Core Department of Biostatistics Harvard School of Public Health 655 Huntington Avenue Boston, MA 02115 [EMAIL PROTECTED] >>> "Weiwei Shi" <[EMAIL PROTECTED]> 08/2

Re: [R] [BioC] similarity between two gene lists with varied length

Hi Weiwei, You may want to have a look at the Bioconductor package OrderedList. It searches for similarities in gene rankings without forcing the user to specify a threshold, where to cut the lists. Hope this helps, Cheers, Claudio -Original Message- From: "Weiwei Shi" [mailto:[EMAI

Re: [R] [BioC] similarity between two gene lists with varied length

Hi, Weiwei, I think you can try fisher exact test simply. Take all genes of your organism as sample pool and your question is that: when you selected two gene lists from the sample pool, how to judge the independence of the two gene lists. The fisher exact test worked for this type of question. B

Re: [R] [BioC] similarity between two gene lists with varied length

Actually, making this question more nontrivial is, 1. the lengths for the two gene lists are very different; 2. I could add another list as gene weight to any gene, for example, of union of two gene lists. On Sun, Aug 24, 2008 at 9:15 AM, Shannon, William <[EMAIL PROTECTED]>wrote: > First thought