Hi,
I had a question on using fitPLM to determine quality of chips.

I run fitPLM and obtain the weights etc. from the pset object.
>From this, I compute the percentage of probes with weight less than one for
every chip,  and if that percentage is greater than say 20%  (empirically
determined), I consider the chip as failing quality.
So out of 10 chips, I get say 8 good chips.

Now, if I take these 8 good chips from the first run and do a fitPLM again
and I use the percentage of weights idea above to determine pass/fail, I get
a few of these good chips to fail again. It seems that for a given set of
chips, there are always probes which will have weights less than one.
So I was wondering if this is a good measure for quality testing.

I looked at the distribution of the residuals over all chips from the first
run and the distribution from the second run and the spread in the second
distribution is much less, as expected.

Thanks for any help/suggestions.

Dhruv

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