Question

How to choose the most 2 different samples in an array experiment

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Ali Mohammadian ▴ 290

@ali-mohammadian-5008

Last seen 9.6 years ago

Dear all, What test should be done on ~40 samples, each in triplicate, to determine which sample is the most different to all samples? and What test should be done to determine the two samples which are most different?

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ADD COMMENT • link updated 12.1 years ago by boczniak767 ▴ 720 • written 12.1 years ago by Ali Mohammadian ▴ 290

score 0 · Answer 1 · 2012-03-15

Hi, On Thursday, March 15, 2012, Ali Mohammadian <nrcgeb@gmail.com> wrote: > Dear all, > > What test should be done on ~40 samples, each in triplicate, to > determine which sample is the most different to all samples? It's not a test, per se, but if I recall corrextly, the arrayQualityMetrics package has a figure which shows distances between arrays as a heat map, followed by "outlier" (by distance) detection. Perhaps you can take inspiration from that. -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact [[alternative HTML version deleted]]

score 0 · Answer 2 · 2012-03-15

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boczniak767 ▴ 720

@maciej-jonczyk-3945

Last seen 24 days ago

Poland

Hi Ali, >What test should be done to determine the two samples which are >most different? PCA (Principal component analysis) would be perfect for this purpose. There are some packages from bioconductor, R which performs it. HTH, Maciej Jo?czyk -- Maciej Jonczyk, Department of Plant Molecular Ecophysiology Faculty of Biology, University of Warsaw 02-096 Warsaw, Miecznikowa 1 Poland -- This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com

ADD COMMENT • link 12.1 years ago boczniak767 ▴ 720

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pcaMethods combined with rggobi is particularly good for this purpose. On Thu, Mar 15, 2012 at 10:18 AM, Maciej JoÅczyk <mjonczyk@biol.uw.edu.pl>wrote: > Hi Ali, > > > What test should be done to determine the two samples which are >> most different? >> > > PCA (Principal component analysis) would be perfect for this purpose. > There are some packages from bioconductor, R > which performs it. > > HTH, > Maciej JoÅczyk > > -- > Maciej Jonczyk, > Department of Plant Molecular Ecophysiology > Faculty of Biology, University of Warsaw > 02-096 Warsaw, Miecznikowa 1 > Poland > > > > -- > This email was Anti Virus checked by Astaro Security Gateway. > http://www.astaro.com > > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]

ADD REPLY • link 12.1 years ago Tim Triche ★ 4.2k