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List:       bioconductor
Subject:    Re: [BioC] =?utf-8?q?Any_package_like_genefilter_for_NGS=3F?=
From:       "=?utf-8?B?WGlhb2h1aSBXdQ==?=" <wux3 () muohio ! edu>
Date:       2010-08-31 20:13:34
Message-ID: 201008311613325946781 () muohio ! edu
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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@muohio.edu<mailto: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

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