Detection calls and LIMMA
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avehna ▴ 240
@avehna-3930
Last seen 9.6 years ago
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]]
Microarray Microarray • 809 views
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
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 at 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
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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]]
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