[BioC] LPE

[Harry Hurd]

Hello,

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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