[Bioperl-microarray] Re: Bio::Microarray

[Allen Day]

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/
> 
> 
>