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RE: st: how to deal with censoring at zero (a lot of zeroes) for a laboratory re


From   "Daniel Waxman" <dan@amplecat.com>
To   <statalist@hsphsun2.harvard.edu>
Subject   RE: st: how to deal with censoring at zero (a lot of zeroes) for a laboratory re
Date   Mon, 6 Jun 2005 07:17:01 -0400

Maarten, Kevin,

Thank you very much for your replies.  So for now I am just going give up
trying to make distributional assumptions and to drop the half of the
observations which are zero or non-detectable prior to log transforming the
predictor and to creating the logistic model.  In fact, whether I do this or
change the zero to half of the lowest detectable value (i.e. .005) doesn't
have much of an effect on the logistic odds ratio.

If anybody has any objections to this (or sees how a statistical reviewer
for a medical journal might have objections), please let me know.

Daniel

-----Original Message-----
From: owner-statalist@hsphsun2.harvard.edu
[mailto:owner-statalist@hsphsun2.harvard.edu] On Behalf Of maartenbuis
Sent: Sunday, June 05, 2005 7:38 PM
To: statalist@hsphsun2.harvard.edu
Subject: Re: st: how to deal with censoring at zero (a lot of zeroes) for a
laboratory re

I am tired: The cirtical assumption behind Multiple Imputation is that
the probability of missingness does not depend on the value of the
missing variable itself (Missing At Random, or MAR). This is obviously
not the case with censoring. My objection against (conditional) mean
imputation, and my remark about selecting on the independent variables
still hold. So, given that you have a large number of observations, I
would just ignore the zero observations.

Maarten 

--- In statalist@yahoogroups.com, "maartenbuis" <maartenbuis@y...> wrote:
> Hi Daniel,
> 
> It looks to me like you could use -tobit- for log(tropin) and just a
> constant. The predicted values should give you the extrapolations you
> want. (This will be the same value for all missing observations: the
> mean of the log-normal distribution conditional on being less than the
> censoring value)
> 
> However, These are actually missing values, and apperently you want to
> create imputations for them. If you just use the values you obtained
> from -predict- you will be assuming that you are as sure about these
> values as you are about the values you actually observed, and thus get
> standard errors that are too small. If you really want to impute, than
> you could have a look at -mice- (findit mice). Alternatively, you
> could use the results from -tobit- to generate multiple imputations.
> Mail me if you want to do that, and I can write, tonight or tomorrow,
> an example for the infamous auto dataset. However, censoring on the
> independent variable is generally much less a problem than censoring
> on the dependent variable, so ignoring (throwing away) the censored
> observation, should not lead to very different estimates.
> 
> HTH,
> Maarten
> 
> --- "Daniel Waxman" <dan@a...> wrote:
> > I am modeling a laboratory test (Troponin I) as an independent 
> > (continuous) predictor of in-hospital mortality in a sample of 
> > 10,000 subjects.  <snip> The problem is the zero values, what they 
> > represent, and what to do with them.   The distribution of results 
> > ranges from the minimal detectable level of .01 mcg/L to 94 mcg/L, 
> > with results markedly skewed to the left (nearly half the results 
> > are zero; 90% are < .20.  results are given in increments
> > of .01).  Of course, zero is a censored value which represents a
> > distribution of results between zero and somewhere below .01.
> <snip.
> > I found a method attributed to A.C. Cohen of doing essentially this 
> > which uses a lookup table to calculate the mean and standard 
> > deviation of an assumed log-normal distribution based upon the 
> > non-censored data and the proportion of data points that are 
> > censored, but there must be a better way to do this in Stata.
> > 
> > Any thoughts on (1) whether it is reasonable to assume the 
> > log-normal distribution (I've played with qlognorm and plognorm, but
> > it's hard to know what is good enough), and if so (2) how to do it?  
> 
> 
> 
> 
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