[BioC] removal of genes with low expression values

Robert Gentleman rgentlem at gmail.com
Thu Jul 8 19:32:38 CEST 2010


Hi,


On Wed, Jul 7, 2010 at 6:22 AM, Naomi Altman <naomi at stat.psu.edu> wrote:
> Isn't filtering on spread like pretesting for differential expression?
>  Maybe not such a good idea.

  No it isn't like pretesting and it is quite often a good idea.
Please have a look at:

Independent filtering increases detection power for high-throughput experiments.
Bourgon R, Gentleman R, Huber W.
Proc Natl Acad Sci U S A. 2010 May 25;107(21):9546-51. Epub 2010 May 11.
 Where the reasons why it is not like a pretest are given and the
potential benefits are laid out.



>
> When using MAS5, it is traditional to use the Affy presence/absence score.
>  (Not necessarily optimal ...)
>
> --Naomi
>
> At 06:53 AM 7/7/2010, Yuan Hao wrote:
>>
>> 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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>>
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>
> Naomi S. Altman                                814-865-3791 (voice)
> Associate Professor
> Dept. of Statistics                              814-863-7114 (fax)
> Penn State University                         814-865-1348 (Statistics)
> University Park, PA 16802-2111
>
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>



-- 
Robert Gentleman
rgentlem at gmail.com



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