|
From: Michael P. <mic...@ho...> - 2001-02-01 21:49:25
|
----- 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 |