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

[Junmin L. <ju...@pc...>]

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
>