[R] Qvalue package: I am getting back 1, 000 q values when I only want 1 q value.

[Jay Tanzman]

What you're doing makes no sense.  Given p-values p_i, i=1...n, resulting
from hypothesis tests t_i, i=1...n, the q-value of p_i is the expected
proportion of false positives among all n tests if the significance level
of each test is α=p_i. Thus a q-value is only defined for an observed
p-value.  Assuming that you have stored n observed p-values in an R vector
P, and the ith p-value P[i]==.05, then the R syntax to obtain the q-value
for P[i] is qvalue(P)$qvalues[i].

If, instead (as I suspect), that .05 is not among your observed p-values,
but you want to know what the FDR would be, given your sequence of
p-values, if the significance level of every test were .05, then the R
syntax would be
max(qvalue(P)$qvalues[P<=.05]).

On Fri, Jan 13, 2017 at 2:08 AM, Thomas Ryan <tombernardryan at gmail.com>
wrote:

> Jim,
>
> Thanks for the reply. Yes I'm just playing around with the data at the
> minute, but regardless of where the p values actually come from, I can't
> seem to get a Q value that makes sense.
>
> For example, in one case, I have an actual P value of 0.05.  I have a list
> of 1,000 randomised p values: range of these randomised p values is 0.002
> to 0.795, average of the randomised p values is 0.399 and the median of the
> randomised p values is 0.45.
>
> So I thought it would be reasonable to expect the FDR Q Value (i.e the
> number of expected false positives over the number of significant results)
> to
> be at least over 0.05, given that 869 of the randomised p values are >
> 0.05?
>
> When I run the code:
>
> library(qvalue)
> list1 <-scan("ListOfPValues")
>
> qobj <-qvalue(p=list1)
>
> qobj$pi0
>
>
> The answer is 0.0062. That's why I thought qobj$pi0 isn't the right
> variable to be looking at? So my problem (or my mis-understanding) is that
> I have an actual P value of 0.05, but then a Q value that is lower, 0.006?
>
>
> Thanks again for your help,
>
> Tom
>
>
>
>
>
>
>
>
> On Thu, Jan 12, 2017 at 9:27 PM, Jim Lemon <drjimlemon at gmail.com> wrote:
>
> > Hi Tom,
> > From a quick scan of the docs, I think you are looking for qobj$pi0.
> > The vector qobj$qvalue seems to be the local false discovery rate for
> > each of your randomizations. Note that the manual implies that the p
> > values are those of multiple comparisons within a data set, not
> > randomizations of the data, so I'm not sure that your usage is valid
> > for the function..
> >
> > Jim
> >
> >
> > On Fri, Jan 13, 2017 at 4:12 AM, Thomas Ryan <tombernardryan at gmail.com>
> > wrote:
> > > Hi all, I'm wondering if someone could put me on the right path to
> using
> > > the "qvalue" package correctly.
> > >
> > > I have an original p value from an analysis, and I've done 1,000
> > > randomisations of the data set. So I now have an original P value and
> > 1,000
> > > random p values. I want to work out the false discovery rate (FDR) (Q;
> as
> > > described by Storey and Tibshriani in 2003) for my original p value,
> > > defined as the number of expected false positives over the number of
> > > significant results for my original P value.
> > >
> > > So, for my original P value, I want one Q value, that has been
> calculated
> > > as described above based on the 1,000 random p values.
> > >
> > > I wrote this code:
> > >
> > > pvals <- c(list_of_p_values_obtained_from_randomisations)
> > > qobj <-qvalue(p=pvals)
> > > r_output1 <- qobj$pvalue
> > > r_output2 <- qobj$qvalue
> > >
> > > r_output1 is the list of 1,000 p values that I put in, and r_output2 is
> > a q
> > > value for each of those p values (i.e. so there are 1,000 q values).
> > >
> > > The problem is I don't want there to be 1,000 Q values (i.e one for
> each
> > > random p value). The Q value should be the false discovery rate (FDR)
> > (Q),
> > > defined as the number of expected false positives over the number of
> > > significant results. So I want one Q value for my original P value, and
> > to
> > > calculate that one Q value using the 1,000 random P values I have
> > generated.
> > >
> > > Could someone please tell me where I'm going wrong.
> > >
> > > Thanks
> > > Tom
> > >
> > >         [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
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> > > 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.
>

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