Re: [Gusdev-rad-issues] Error loading data using ArrayResultLoader

[Sucheta T. <su...@vb...>]

Hello,

Can some one please point me to the site, where I get the newest version
of RAD plugins. I guess I have older version.

I did not get it in CBIL repository.

Thanks

Sucheta



> Hi, Sucheta,
> Attached is the testing dataset I used to run the plugin, basically I used
> the exact same header as yours and put one line of data and run it using
> the same command line as yours.
>
> The plugin runs OK. I can almostly conclude that something is wrong with
> your data file.
>
> BTW,  you never use these two options together "--debug --commit", for it
> doesn't make sense. Normally you run the plugin  without  the "--commit"
> mode to make sure everything is right. then you run it  using "--commit"
> mode. "--debug" mode is for debugging purpose.
>
> The following steps demonstrate the good pratice of using plugin:
>
> 1. run it with small test.dat w/o --commit
> ga GUS::RAD::Plugin::ArrayResultLoader --data_file test.dat --array_id 3
> --e_subclass_view ShortOligo --c_subclass_view ShortOligoFamily
> --quantification_id 3 --er_subclass_view AffymetrixCEL --cr_subclass_view
> AffymetrixMAS5
>
> 2. if there is problem, add the --debug option
> ga GUS::RAD::Plugin::ArrayResultLoader --data_file test.dat --array_id 3
> --e_subclass_view ShortOligo --c_subclass_view ShortOligoFamily
> --quantification_id 3 --er_subclass_view AffymetrixCEL --cr_subclass_view
> AffymetrixMAS5 --debug > & log
>
> 3. probolem solved, use real.dat and --commit option
> ga GUS::RAD::Plugin::ArrayResultLoader --data_file real.dat --array_id
> 3 --e_subclass_view ShortOligo --c_subclass_view ShortOligoFamily
> --quantification_id 3 --er_subclass_view AffymetrixCEL --cr_subclass_view
> AffymetrixMAS5 --commit > & log
>
>
> ---junmin
>
>
>
> On Mon, 15 Nov 2004, Elisabetta Manduchi wrote:
>
>>
>> Hi Sucheta,
>> I'm cc-ing Junmin on this, since he wrote the plugin, so he should be
>> able to
>> pin down the problem.
>> Elisabetta
>>
>>
>> ---
>>
>> On Mon, 15 Nov 2004, Sucheta Tripathy wrote:
>>
>>>
>>>
>>> Hi Elissabetta,
>>>
>>> I am trying to upload data using the ArrayResultLoader plugin and
>>> following are my command line parameters
>>>
>>> ga GUS::RAD::Plugin::ArrayResultLoader --data_file <path> --array_id 3
>>> --e_subclass_view ShortOligo --c_subclass_view ShortOligoFamily
>>> --quantification_id 3 --er_subclass_view AffymetrixCEL
>>> --cr_subclass_view
>>> AffymetrixMAS5 --debug --commit >& result_loader.err
>>>
>>>
>>> And my data file has the following heeader:
>>>
>>> x_position y_position mean stdv name detection signal detection_p_value
>>> data        data       data  data  data  data   data   data
>>>
>>> All separated by tab.
>>>
>>> But I get an error like this:
>>>
>>> Missing header x_position which is required to upload data into file.
>>>
>>> Although I have the x_position defined in the header.
>>>
>>> Am doing something wrong here. I have all the pre-requisites done.
>>>
>>> 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