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

[Laurent Gautier]

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
it. 


> Thanks everyone for your help


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

> Josh
> 


Laurent

--------------------------------------------------------------
Laurent Gautier			CBS, Building 208, DTU
PhD. Student			D-2800 Lyngby,Denmark	
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