Re: vpc under PsN
Dear Kajsa and Paolo,
Thanks very much for your explanation. I would try to delete the -predcorr
option in the command line and run the vpc again. But another question is,
if I spotted an unusual point in one of the VPC runs with (-predcorr), is
it possible to detect this observation in the original data set, so that I
might be able to see where the problem is? Thank you.
Best Regards
Quoted reply history
On 28 June 2014 02:12, Kajsa Harling <[email protected]> wrote:
> Hi Xinting,
>
> The file vpctab is intended solely as input to Xpose when visualizing the
> vpc, it is not the table file described in the userguide. If you want to
> see the table files you should look at the *npctab.dta files in the m1
> subdirectory.
>
> Best regards,
> Kajsa
>
>
> On 06/27/2014 05:17 PM, Paolo Denti wrote:
>
> Hi Xinting,
> if you used -predcorr when creating the VPC, your DVs in each bin will be
> rescaled using their own PRED and the median PRED in that bin, so you won't
> be able to find the exact value in your original dataset.
> As for the ID renumbering, I am not able to comment, but I would post this
> on the user list for PsN, where they may be able to help.
>
> Until you get an answer, I would simply suggest re-running the VPC without
> -predcorr and spot the outliers with that, if they are still visible. This
> way you could also try to infer whether the outlier values were introduced
> with the rescaling for the pred-correction, or they were there already in
> the original data.
>
> My experience is that pred-corrected VPCs may introduce unduly large
> rescaling when the bin is large and the concentration profile changes a lot
> within that bin. Think of the extreme case of a delay in absorption (or a
> very sharp transit absorption): samples drawn before or after the delay
> will have wildly different PREDs, and will thus be scaled very differently,
> cuz the scaling factor is not calculated for the median PRED at the time of
> the sample that is rescaled, but for the median PRED throughout the bin.
>
> I hope this helps you sort out your problem, and I would welcome other
> people's comment on this implementation of PC-VPC (or on my
> misunderstanding).
> Ciao,
> Paolo
>
> On 2014/06/27 15:47, Xinting Wang wrote:
>
> Dear all,
>
>
>
> I am new to vpc and have a basic technical question regarding the vpc
> under PsN to ask.
>
>
>
> Currently I am doing a vpc to validate a model, whose data was constructed
> in such a way that the dependent variable is log-transformed and labeled
> LNDV. The original model was built with data from both healthy subject as
> well as patients, while the vpc separated them. In the first step a plot
> was produced for the healthy subjects in which I found several outlier
> observations. This caused the 97.5% quantile of the observations to have an
> abnormal profile. So I tried to locate the variable, and run a separate vpc
> to check the influence of them.
>
>
>
> I looked up both observations in the vpctab file produced by PsN, and
> tried to look for the points in the model dataset. However to my surprise I
> did not find the observation in the dataset, whether the exact number (DV)
> or the ID. According to the vpc manual the ID is copied exactly from the
> dataset file, but the ID was also not found.
>
>
>
> Could you please help me out of this, as how to locate the points? Thanks
> a million for your kind help. I am attaching the command I am using in the
> vpc for your information:
>
>
>
> vpc final.nmctl -predcorr -lnDV=1 -dv=LNDV -bin_by_count=0
> -bin_array=0.375,0.75,1.5,2.5,4,6,8.5,12,17.5,24.5,35,49,63,77,91
> -stratify_on=STRT -clean=3 -seed=19860322 -samples=200 -run_on_sge
> -sge_queue=all.q -parafile=template.pnm -nodes=30 -sge_prepend="-pe mpich
> 30"
>
>
> Best Regards
>
> --
> Xinting
>
>
> --
> ------------------------------------------------
> Paolo Denti, PhD
> Pharmacometrics Group
> Division of Clinical Pharmacology
> Department of Medicine
> University of Cape Town
>
> K45 Old Main Building
> Groote Schuur Hospital
> Observatory, Cape Town
> 7925 South Africa
> phone: +27 21 404 7719
> fax: +27 21 448 1989
> email: [email protected]
> ------------------------------------------------
>
>
> --
> -----------------------------------------------------------------
> Kajsa Harling, PhD
> System Developer
> Department of Pharmaceutical Biosciences
> Uppsala University
> [email protected]+46-(0)18-471 4308
> http://www.farmbio.uu.se/research/researchgroups/pharmacometrics/
> -----------------------------------------------------------------
>
>
--
Xinting