Hi, what I know so far that this kind of QQ plot is an indication that data has non zero mean: https://stats.stackexchange.com/questions/280634/how-to-interpret-qq-plot-not-on-the-line
but is that an indication that something is wrong with the analysis? Thanks Ana On Tue, Nov 12, 2019 at 2:00 PM Jim Lemon <drjimle...@gmail.com> wrote: > > I thought about this and did a little study of GWAS and the use of > p-values to assess significant associations. As Ana's plot begins at > values of about 0.001, this seems to imply that almost everything in > the genome is associated to some degree. One expects that most SNPs > will not be associated with a particular condition (p~1), so perhaps > something is going wrong in the calculations that produce the > p-values. > > Jim > > On Wed, Nov 13, 2019 at 12:28 AM Patrick (Malone Quantitative) > <mal...@malonequantitative.com> wrote: > > > > I agree with Abby. That would defeat the purpose of a QQ plot. > > > > On Mon, Nov 11, 2019, 9:54 PM Abby Spurdle <spurdl...@gmail.com> wrote: > > > > > Hi > > > > > > I'm not familiar with the qqman package, or GWAS studies. > > > However, my guess would be that you're *not* supposed to change the > > > position of the line. > > > > > > On Tue, Nov 12, 2019 at 11:48 AM Ana Marija <sokovic.anamar...@gmail.com> > > > wrote: > > > > > > > > Hi, > > > > > > > > I was using this library, qqman > > > > https://cran.r-project.org/web/packages/qqman/vignettes/qqman.html > > > > > > > > to create QQ plot, attached. How would I change this default abline to > > > > start from the beginning of my QQ line? > > > > > > > > This is my code: > > > > qq(dd$P, main = "Q-Q plot of GWAS p-values") > > > > > > > > Thanks > > > > Ana > > > > ______________________________________________ > > > > 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. > > > > > > ______________________________________________ > > > 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. > > ______________________________________________ > 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. ______________________________________________ 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.
