Dear Wolfgang,

Thank you for your response, I agree with you. I will read the paper now...

Best Regards,
Avhena

On Mon, Feb 28, 2011 at 4:38 AM, Wolfgang Huber <whuber@embl.de> wrote:

> Hi Avhena
>
> it is not required, but properly applied filtering can increase detection
> power in your experiment while still controlling type-I error (false
> positives). The example you mention seems to be one that you want to keep
> though, since it is a good candidate for being up-regulated in the Treatment
> condition. One possibly reasonable criterion would be, e.g., to filter out
> all probesets that are called 'Absent' on all arrays. Some further
> discussion on the topic is also here:
>
> [1] Bourgon, Gentleman and Huber. Independent filtering increases detection
> power for high-throughput experiments. PNAS, 107(21):9546-9551,
>
>        Best wishes
>        Wolfgang
>
>
> Il Feb/28/11 6:51 AM, avehna ha scritto:
>
>> Hi All,
>>
>> I have a basic question. Is it required to filter the microarray data
>> based
>> on the detection calls (A/M/P) before analyzing it with LIMMA?
>>
>> What if I have the following scenario (for example):
>>
>>                            Control Control Control         Treatment
>> Treatment Treatment
>> 1367813_at           A            A             P
>> P                   P                 P
>>
>> Please note that this gene is just "present/detected"  once in the
>> Control,
>> but it is present in all the replicates of the treatment. In this case:
>> what
>> would be the right thing to do? To eliminate it from the analysis or keep
>> it
>> and consider it up or down depending on the signal of the treatment?
>>
>> Thank a lot!
>> Avhena
>>
>>        [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
> --
>
>
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

