Hi all, The genefilter package can be used to filter genes for microarray data, like "find genes whose expression profile is similar to that of specified genes" or " filter genes from a microarray dataset". Now I've many genes detected by NGS data in many conditions, a matrix like [20,000 genes*30 condistions], each element is the read count for that gene. The matrix is too huge for headmap function in R to cluster these genes. So I think I need to filter some genes or discard some useless genes first. Is there any package like genefilter for NGS or some ideas on how to filter the genes? Thank you! Regards, Xiaohui [[alternative HTML version deleted]]

On Tue, Aug 31, 2010 at 12:19 PM, Xiaohui Wu <wux3@muohio.edu> wrote: > Hi all, > > The genefilter package can be used to filter genes for microarray data, > like "find genes whose expression profile is similar to that of specified > genes" or " filter genes from a microarray dataset". Now I've many genes > detected by NGS data in many conditions, a matrix like [20,000 genes*30 > condistions], each element is the read count for that gene. The matrix is > too huge for headmap function in R to cluster these genes. So I think I need > to filter some genes or discard some useless genes first. Is there any > package like genefilter for NGS or some ideas on how to filter the genes? > > Hi, Xiaohui. I think that you will find that most if not all of the methods in the genefilter package will accept a matrix and it sounds like that is what you have. Sean [[alternative HTML version deleted]]