I agree with Abby. That would defeat the purpose of a QQ plot. On Mon, Nov 11, 2019, 9:54 PM Abby Spurdle <spurdle.a at 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.anamarija at 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$P, main = "Q-Q plot of GWAS p-values") > > > > Thanks > > Ana > > ______________________________________________ > > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >[[alternative HTML version deleted]]
I thought about this and did a little study of GWAS and the use of p-values to assess significant associations. As Ana's plot begins at values of about 0.001, this seems to imply that almost everything in the genome is associated to some degree. One expects that most SNPs will not be associated with a particular condition (p~1), so perhaps something is going wrong in the calculations that produce the p-values. Jim On Wed, Nov 13, 2019 at 12:28 AM Patrick (Malone Quantitative) <malone at malonequantitative.com> wrote:> > I agree with Abby. That would defeat the purpose of a QQ plot. > > On Mon, Nov 11, 2019, 9:54 PM Abby Spurdle <spurdle.a at gmail.com> wrote: > > > Hi > > > > I'm not familiar with the qqman package, or GWAS studies. > > However, my guess would be that you're *not* supposed to change the > > position of the line. > > > > On Tue, Nov 12, 2019 at 11:48 AM Ana Marija <sokovic.anamarija at gmail.com> > > wrote: > > > > > > Hi, > > > > > > I was using this library, qqman > > > https://cran.r-project.org/web/packages/qqman/vignettes/qqman.html > > > > > > to create QQ plot, attached. How would I change this default abline to > > > start from the beginning of my QQ line? > > > > > > This is my code: > > > qq(dd$P, main = "Q-Q plot of GWAS p-values") > > > > > > Thanks > > > Ana > > > ______________________________________________ > > > R-help at 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 at 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 at 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.
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 <drjimlemon at 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) > <malone at 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 <spurdle.a at 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.anamarija at 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 at 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 at 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 at 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 at 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.
Just a small comment. In GWAS studies p values are considerate to bi significant whwn p < 10-6 or smaller regards, Milo? On Tue, 12 Nov 2019 at 21:00, Jim Lemon <drjimlemon at 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) > <malone at 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 <spurdle.a at 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.anamarija at 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 at 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 at 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 at 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 at 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]]
As this is O/T I'll keep it offlist. Inline: On Tue, Nov 12, 2019 at 12:00 PM Jim Lemon <drjimlemon at 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. >Exactly! Or possibly with the data handling pipeline prior to getting into R. -- Bert> > Jim > > On Wed, Nov 13, 2019 at 12:28 AM Patrick (Malone Quantitative) > <malone at 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 <spurdle.a at 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.anamarija at 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 at 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 at 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 at 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 at 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]]
On 12/11/2019 2:56 p.m., Jim Lemon 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.I may be misunderstanding your last sentence, but if there is no association, the p-value would usually have a uniform distribution from 0 to 1, it wouldn't be near 1. I'd guess we're not seeing the p values from every test, only those that are less than 0.001. If that's true, and there are no effects, it makes sense to multiply all of them by 1000 to get U(0,1) values. On the plot, that would correspond to subtracting 3 from -log10(p), or adding 3 to the reference line, as Ana requested. Or just multiply them by 1000 and pass them to qq(): qq(dd$P*1000, main = "Q-Q plot of small GWAS p-values") As far as I can see, there's no way to tell qqman::qq to move the reference line. Duncan Murdoch> > Jim > > On Wed, Nov 13, 2019 at 12:28 AM Patrick (Malone Quantitative) > <malone at 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 <spurdle.a at 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.anamarija at 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 at 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 at 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 at 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 at 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. >