Re: vpc under PsN
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
Quoted reply history
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]