[BioC] Re: Bioconductor Digest, Vol 10, Issue 27

[Eric]

As far as I know, the only way to reduce both Type I and Type II error 
simultaneously is to increase the power. This is usually done by increasing 
the N, but arguments have been made for increasing power using pooling 
strategies. In any case, this happens at the design stage, not the analysis 
stage.
At 12:00 PM 12/16/2003 +0100, you wrote:
>Message: 3
>Date: Tue, 16 Dec 2003 09:46:50 -0000
>From: "michael watson (IAH-C)" <michael.watson at bbsrc.ac.uk>
>Subject: RE: [BioC] ttest or fold change
>To: "'Baker, Stephen'" <Stephen.Baker at umassmed.edu>,
>         bioconductor at stat.math.ethz.ch
>Message-ID:
>         <20B7EB075F2D4542AFFAF813E98ACD93028224D6 at cl-exsrv1.irad.bbsrc.ac.uk>
>Content-Type: text/plain;       charset="iso-8859-1"
>
> >This seems small but with a microarray with thousands of genes, this
> >easily produces a bunch of false positives. I looked at 10 chips from a
> >real control group arbitrarily labeling 5 chips as control and 5 as
> >experimental.  I would by theory expect 35 false positives and got
> >exactly 32, that is 32 sitations in which all the low ranks were in one
> >group and the high ranks in the other.  For a chip with 22000 genes, you
> >would expect 175 false positive results by this criteria. Standard
> >statistical methods would give you a specified type I error rate that
> >you can count on, it would have found NONE of the genes significant
> >(i.e. bonferroni adjustment)
>
>A truly excellent reply, and one which I will no doubt refer to 
>frequently; I am still
>very much a novice statistician.  However, and please correct me if I am 
>wrong, but
>I presume that some scientists are equally afraid of false negatives as 
>false positives?
>i.e. that if we are so conservative such that we try to ENSURE that there 
>are NO
>false positives, we may throw away genes as not differentially expressed 
>when in
>reality they are?  It will be interesting to have a discussion on this - 
>is it possible,
>using statistics, to guarentee both no false positives and no false 
>negatives?  If not,
>then surely the investigator must decide which is relevant to the study in 
>question before
>going on to decide which stats to use.

Eric Blalock, PhD
Dept Pharmacology, UKMC
859 323-8033

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