[BioC] removal of genes with low expression values
Yuan Hao
yuan.x.hao at gmail.com
Wed Jul 7 12:53:23 CEST 2010
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
>
> [[alternative HTML version deleted]]
>
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