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

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

Sucheta,
from the Sanger cvs:
http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/GUS/RAD/plugin/perl/?cvsroot=GUS&f=h

Elisabetta

---

On Mon, 15 Nov 2004, Sucheta Tripathy wrote:

> 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
>