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]]