Re: QSAR - Rank order of activity data

Hello again, Jim:

Are you rank-transforming the descriptors as well? The all-way rank transform
has the great benefit of converting all monotonic relationships to linear ones,
but it is slightly tricky to do external predictions and complicated to do
cross-validation without leaving (potentially) problematic "holes" in the data
matrix. That said, I am glad to see nonparametric QSAR being discussed here. I
confess to having a soft spot in my heart for the subject ever since my grad
school days at Cornell.

Bob Clark
Tripos, Inc.

james.metz|-|abbott.com wrote:
>
> QSAR Society Colleagues,
>
> I would like to convert biological activity or molecular property data
> to a rank order e.g., convert IC50 or p(IC50) data to a
> statistically meaningful rank order.
>
> This may sound like a problem with a simple answer, but apparently is
> not for several reasons:
>
> 1) The trivial approach of simply sorting compounds by p(IC50) and
> then assigning a rank leads to artificial rank distinctions among
> compounds that given the inherent experimental variability of the data is
> probably not justified.
>
> 2 If one had replicates for every IC50, one could attempt to do
> T-tests between every IC50, and assign a new rank if the statistic exceeds the
> 95% confidence level. However, I do not have replicates for every measured
> IC50 value.
>
> 3) If one attempts to normalize the IC50 distribution and then assign
> ranks, perhaps, on the basis of mean +/- n*sigma values, this
> creates "somewhat" artificial ranks where some compounds may have been right
> at the border of the mean + sigma, or mean + 2*sigma, etc.
>
> If anyone has ideas, experience, or suggestions on this topic, I
> welcome your comments !
>
> Regards,
> Jim Metz
>
> James T. Metz, Ph.D.
> Research Investigator Chemist
>
> GPRD R46Y AP10-2
> Abbott Laboratories
> 100 Abbott Park Road
> Abbott Park, IL 60064-6100
> U.S.A.
>
> Office (847) 936 - 0441
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>
> james.metz]^[abbott.com
Received on 2003-06-20 - 05:37 GMT