[Bioperl-microarray] RE: Bio::Microarray (fwd)

[Allen Day]

---------- Forwarded message ----------
Date: Mon, 17 Nov 2003 13:53:52 -0500
From: Nigam Shah <nigam at psu.edu>
To: 'Allen Day' <allenday at ucla.edu>
Subject: RE: Bio::Microarray

Hi! Allen,

Here is the module, along with a test script Test_Gpr.pl and 5 files
required for the test. The Test_Gpr.pl has explainations as to what each
function does and what input they needs. There will be two output files
written.

Regards,
Nigam.


%-----Original Message-----
%From: Allen Day [mailto:allenday at ucla.edu] 
%Sent: Monday, November 17, 2003 12:25 PM
%To: Nigam Shah
%Cc: bioperl-microarray at bioperl.org
%Subject: Re: Bio::Microarray
%
%
%Nigam,
%
%That's excellent.  I'm CCing this mail to the 
%bioperl-microarray mailing 
%list, as others may have comments.  Can you please attach a 
%copy of your 
%modules in your reply so I can take a look at what you have?
%
%-Allen
%
%
%On Mon, 17 Nov 2003, Nigam Shah wrote:
%
%> Hi! Allen,
%> 
%> I have written a module for Reading and processing GenePix 
%GPR files. 
%> I contacted Brian Osborn and he suggested I get in touch 
%with you. The 
%> module can do the following:
%> 
%> 1- read a GPR file
%> 2- ouput user specified columns
%> 3- cross check the GPR file with GAL file (Gene array list file)
%> 4- output the GPR file header
%> 5- Flag data rows using six different quality filters
%> 6- calculate normalization factors (Spike and whole chip)
%> 7- Normalize the data and write user selected columns in output
%> 8- give a Ratio-Intensity plot (a very commonly used QC plot) for:
%>         - all spots
%>         - unflagged spots
%>         - positive control spots (spikes)
%> 
%> I need some help about how to write documentation, write tests and 
%> other conventions to follow to contribute it under Bio::microarray.
%> 
%> Regards,
%> Nigam.
%> 
%> 
%> Nigam Shah
%> Graduate Fellow,
%> Huck Institute for Life Sciences,
%> Penn State University.
%> Ph:(814)863-5720
%> Web: www.personal.psu.edu/nhs109/
%> 
%> 
%> 
%
%
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