[GeneX-dev] CyberT questions...

[Michael P. <mic...@ho...>]

----- Original Message -----
From: Michael Pear
To: Harry Mangalam
Sent: Thursday, February 01, 2001 1:13 PM
Subject: CyberT questions...


Hi Harry,
 I've massaged the data here to analyze the dataset with CyberT. I'm left
with a few questions
that I hope you can help with.

1) I'm left with the impression that there was a problem with the CyberT
scripts that you are addressing
to ensure negatives cannot get passed to cyberT. Is that correct? That would
certainly make operation
more bulletproof.

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.

3) Is there any description of the details of the Bayesian approach or other
formulas used in cyberT?
---other than the R code, which I haven't had a chance to really take on and
understand....not ANOTHER
language, pleeeease....I'm reaching saturation :-(

4) I'm wondering about including the full description for genes in the
cyberT output and xgobi (for identification). I would expect it to be a
rather simple change to have the output data include the description rather
than gene name...any reason to expect that this mod would give problems? Do
you have any plans in this regard for future versions?

Regards,

Michael Pear