[BioC] removal of genes with low expression values

[Yuan Hao]

Usually it can be filtered based on IQR and/or variance across  
samples, which might be worthy of thinking besides 'average'

Yuan

On 7 Jul 2010, at 11:47, Sean Davis wrote:

> On Wed, Jul 7, 2010 at 6:28 AM, Hernando Martínez <hernybiotec at gmail.com 
> >wrote:
>
>> Hi, I need to remove genes with low expression values from a  
>> expression
>> matrix. I would like to remove those with an average of expression  
>> values
>> less than a certain cut-off. I was thinking in computing the  
>> average for
>> each row, create a list with the gene names for which their average  
>> is less
>> than the cut-off, and remove those genes from the initial matrix.  
>> However,
>> I
>> have a couple of doubts that maybe you can help me with. Is there any
>> package or function that makes this easier? And, does anyone know  
>> which
>> cut-off to use for data normalized with RMA and for data normalized  
>> with
>> MAS5? Thanks,
>>
>>
> Take a look at the genefilter package.  However, what you describe  
> can be
> done easily with standard R.
>
> I don't think there is such a thing as a "standard" cutoff for  
> microarray
> data.
>
> Sean
>
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