Re: [Gusdev-rad-issues] Re: [Gusdev-gusdev] about uploading RAD data problem

[Elisabetta M. <man...@pc...>]

Hi Sucheta,
if you go to http://www.cbil.upenn.edu/RAD/php/RAD-installation.php? and 
look under point 2 you will see the flow of the RAD pipeline that we have 
for our instance of RAD.
Summarizing, before you can load the results for a given quantification: 
the study must have been created, the assay, acquisition, and 
quantification entries have to be present in the db (and the array itself 
too since assay points to it).
The array can be loaded via the ArrayLoader plugin. All of the rest
can be loaded using the suite of webforms StudyAnnotator 
(whose code we make available). It's enough to complete the annotation in 
Module I (From assay to quantification) in order to get to the point where 
the results can be loaded, the remaining annotation can be done 
subsequently.
Alternatively, the above entries can be inserted into the database via a 
plugin. For the case of MAS5 data we have recently developed a new plugin 
that automatically enteres all the information for Module I by reading the 
.EXP and .RPT files (I gather one can ask GCOS to output these files too). 
This plugin is not in the Sanger cvs as it contains brief parts that are 
specific to our instance of RAD, but we can make it available upon 
request to those who would like to use it, after they modify those parts 
to suit their instances.
Elisabetta

On Tue, 4 May 2004, Sucheta Tripathy wrote:

> 
> Hi Elissabetta,
> 
> For me to use ArayResultLoader.pm , I have to first upload data into
> several other parent tables i.e; RAD3:ElementImp,
> RAD3::Array,
> RAD3::OntologyEntry and all the child tables of RAD3::Array.
> 
> Which plugin do I use to do all that?
> 
> Thanks
> 
> Sucheta
> --
> Sucheta Tripathy
> Virginia Bioinformatics Institute Phase-I
> Washington street.
> Virginia Tech.
> Blacksburg,VA 24061-0447
> phone:(540)231-8138
> Fax:  (540) 231-2606