I believe that a much better place to ask this is on the Bioconductor Support Site:
https://support.bioconductor.org/ Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Wed, Mar 4, 2020 at 9:51 PM Bogdan Tanasa <tan...@gmail.com> wrote: > Dear all, > > please would you let me know, is there a package in R that has > implemented randomization/permutation > tests for joint genomic analyses > > (an example of joint genomic analyses -- when jointly considering both GENE > EXPRESSION and PROTEIN BINDING along the DNA). > > The context of my question is the following : > > let's consider 1000 UP_REGULATED genes with increased PROTEIN X and with a > HISTONE MARK Y : > > in order to show that PROTEIN X is related to HISTONE MARK Y for 1000 > UP-regulated genes, what "controls" would you use for the comparison : > > -- 1000 RANDOM GENES (and multiple randomization tests) > > -- 1000 UP-REG GENES with NO PROTEIN X, NO HISTONE MARK Y > > -- 1000 UP-REG GENES with PROTEIN X, and NO HISTONE MARK Y > > -- 1000 UP-REG GENES with NO PROTEIN X, and with HISTONE MARK Y > > -- 1000 NOT-UP-REG GENES with NO PROTEIN X, NO HISTONE MARK Y > > -- 1000 NOT-UP-REG GENES with PROTEIN X, and NO HISTONE MARK Y > > -- 1000 NOT-UP-REG GENES with NO PROTEIN X, and with HISTONE MARK Y > > -- anything else ? > > thanks a lot, > > bogdan > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
