[BioC] Any package like genefilter for NGS?

[Xiaohui Wu]

Thank you  Sean. I'll have a look at the detail usage of genefilter. Hope it works for my data.

Xiaohui

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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