Thank you Sean. I'll have a look at the detail usage of genefilter. Hope it works for my data. Xiaohui ------------------------------------------------------------- Sean Davis 2010-08-31 14:34:18 Wu, Xiaohui Ms. bioconductor Re: [BioC] Any package like genefilter for NGS? On Tue, Aug 31, 2010 at 12:19 PM, Xiaohui Wu <wux3 at="" muohio.edu<mailto:wux3="" at="" 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