Hi, Instead of using GO or KEGG categories, is it possible to use customerized categories. For example: CC1 : gene1, gene2, gene3 CC2 : gene4, gene5.. instead of GO1: gene1, gene2 I am just wondering which package allows me to give my own defn. of categories. For this purpose, I made a code from basic Hypergeometric {stats} by using dhyper. But what I got is probability from dhyper. However, I really need p-value instead of probability. Should I use phyper instead? Thanks and Merry Xmas! -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

Hi Weiwei, "Weiwei Shi" <helprhelp at="" gmail.com=""> writes: > Instead of using GO or KEGG categories, is it possible to use > customerized categories. For example: > > CC1 : gene1, gene2, gene3 > CC2 : gene4, gene5.. > > instead of > GO1: gene1, gene2 The hyperGTest code in the Category (and more specialized version in the GOstats) package only works with "predefined" categories. Currently, the code supports GO, KEGG, and PFAM. However, the code was designed to be straight forward to extend to add new categories. If you read the source code implementing KEGG and PFAM it should be fairly clear what is needed to add support for a new category. > For this purpose, I made a code from basic Hypergeometric {stats} by > using dhyper. But what I got is probability from dhyper. However, I > really need p-value instead of probability. Should I use phyper > instead? You can also look at how the hyperGTest method is implemented in the Category package. + seth