[BioC] LPE

Jain, Nitin Nitin.Jain at pfizer.com
Mon Mar 14 07:19:51 CET 2005

In LPE, rank-invariant resampling based FDR is used. 

For manuscript of the paper, please visist 

z-scores need not follow N(0,1) distribution.


Nitin Jain, PhD
Non Clinical Statistics
Pfizer, Inc. (Groton, CT)

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Harry Hurd
Sent: Tuesday, February 22, 2005 10:20 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] LPE


We have recently been trying LPE as implemented in bioconductor. We tried it
for N=3 on the affy 133plus array (55K probes). The most significant results
are very pleasing to the biologists (so far anyway) but in trying to do some
further work to assign some FDRs, I plotted the CDF and a normal probability
plot for the resulting z scores.

There is a huge proportion of small values. The zscores do not look anything
like normal.  To what extent should the z scores look N(0,1)?  The estimated
sigma is about .5; should it be near 1?

Does anyone have experience using LPE on a large array like the 133plus? 

Thanks much for any help.

Harry Hurd
Dept of Statistics
UNC Chapel Hill
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