[Fwd: Re: [GeneX-dev] Re: CyberT questions...]

[Harry M. <man...@ho...>]

-------- Original Message --------
Subject: Re: [GeneX-dev] Re: CyberT questions...
Date: Fri, 02 Feb 2001 09:46:52 -0800
From: Harry Mangalam <man...@ho...>
To: gen...@li...
References: <001c01c08c93$cc016ae0$67e...@uc...> <3A7...@ho...> <002a01c08cd3$25a17420$b6e...@ca...>

Hi Michael,

Is this from data passed in directly from a database query? or did you upload it from a file.  The difference is that if it comes in from the DB, some variables are already set (the minrep param is
one of them I think).  

However the fact that minrep is getting set to 2 and that's getting passed to doitall is weird.  I'm checking now..

And attached to this is the replacement 'dendro.jar' file that may fix your applet problem. (actually this has been deleted b/c of the size restriction on the list - I sent it and then I as admin got
the request to approve it... proving the point that idiots rule!)


hjm



Michael Pear wrote:
> 
> > > 2) There appears to be a "minrep" level set to 2 when calling "doitall" that is to prevent
> t-testing on too
> > > small a number of replicates. However, it seems that there is still a "p" value and fold
> computed for  spots
> > > that violate this minimum requirement...am I missing something? We are finding the some of our
> best
> > > "p" values are for spots that do not satisfy the "minrep" requirement.
> >
> > Hmm - that shouldn't be the case - it should refuse to calculate these.  No wonder that they're
> the best p's are with these - they'd tend to have less variability.  This is with the C+E cybert?
> 
> Yes, this is with C+E cybert. I have attached a snippet from the output of one of the runs.
> See, for example, the line "125", which gives a p value of ~.08, but has only one replicate from the
> control set.
> 
> Michael Pear
> 
>   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>                   Name: example.txt
>    example.txt    Type: Plain Text (text/plain)
>               Encoding: quoted-printable

-- 
Cheers,
Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...