[BioC] Filter out genes with small profile variance from gene expression data

[Martin Morgan]

On 03/09/2014 09:00 PM, Jerry Cholo wrote:
>
>
> Hello,
>
>
>
> The following are the command lines that I have been using to filter out
> genes with small profile variance from gene expression data by Matlab.

The genefilter package varFilter function does what you want; base R's apply 
function also does this type of operation. Martin

>
>
>
> ----------------------------------------------------------------------
>
> % filter genes with small profile variance
>
> % less than 25 percentile will be removed from the data
>
> mask = genevarfilter(Data,'Percentile',25);
>
> % Use the mask as an index into the values to remove the filtered data
>
> Data = Data (mask,:);
>
> % GeneSymbols located in the first column of the data
>
> GeneSymbols = GeneSymbols(mask);
>
> ----------------------------------------------------------------------
>
> I need to use R package to perform this task. May someone let me know which
> functions I could use to do all these tasks?
>
>
>
> Thanks,
>
> Jerry
>
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>
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