[BioC] Questions about the Affy package....

Laurent Gautier laurent@cbs.dtu.dk
Tue, 11 Jun 2002 21:24:13 +0200

On Tue, Jun 11, 2002 at 03:31:11PM -0400, Joshua Betcher wrote:
> I have been going through the code for this package and I have a few
> questions and comments:
> 1) For normalize.Plob.loess, slot names that do not exist are used.

..ouch... this is a bug... should be fixed by tomorrow...

> 2)  As I have looked through the help files there does not appear to be any
> examples of the use of the read.cdfile, read.affy, etc..  Does anyone happen
> to have example files that these functions could be used on?

We will try to put examples as soon as possible. If you experience difficulties
with using some the functions, do not hesitate to mail in this very same list.

> 3)  Is there equivalent function to optim in splus?  It was mentioned in the
> code that maybe nlminb could be used; could someone explain this further?

As the comments say, S-plus code was adapted. One particular optimization
function seemed to have no exact equivalent and I did my best to find a
matching one. The comments state it in case somebody wants to noodle with

> Thanks everyone for your help

Thanks for your report. Do not hesitate to mail again...

> Josh


Laurent Gautier			CBS, Building 208, DTU
PhD. Student			D-2800 Lyngby,Denmark	
tel: +45 45 25 24 85		http://www.cbs.dtu.dk/laurent