Re: [Gusdev-rad-issues] question on arrayresultloader plugin

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

Hi Sucheta,
the first thing you need to check is that you are complying with the 
documentation for this plugin, especially in the input data_file format.
HTML documentation can be generated by running the plugin with just the 
--helpHTML option.
If you are using GUS 3.5 this plugin is named LoadArrayResults and 
documentation is also available at 
https://www.cbil.upenn.edu/svn/gus/GusAppFramework/trunk/Supported/doc/LoadArrayResults.html
The usage of this plugin didn't change much from 3.0 to 3.5.

Now, it looks like you are trying to simultaenously load both the .CEL and 
the MAS 5 probe set results. I'm not sure the plugin can handle this, that 
is, you might need to load separately the results for the CEL and the MAS 
5 probeset quantifications (note that they should refer to different 
quantifications). But I'll let JUNMIN  (here cc-ed) confirm on this, as he 
is the author of this plugin. I see that the plugin documentation is not 
clear on this point. 
Here we typically load only the probe_set results in the db (e.g. 
AffymetrixMAS4 or AffymetrixMAS5 or RMAExpress views). For the .cel 
files we simply create a quantification in 
RAD.Quantification for the .cel results with the uri pointing to where we 
hold the .CEL  file in our filesystem.
If loading only the probeset results, the typical header of the data_file 
should be:
name	signal	detection	detection_p_value

(and optionally also stat_pairs and stat_pairs_used)
tab separated, no commas.

In any case, should you still have problems after checking the data 
format, please email Junmin directly. Make sure you include in your email: 
GUS version you are using, command line, top portion of the data_file, any 
error message you get, and description of the problem

Elisabetta
P.S. Note that we also have a batch result loader that works for MAS5 
probe set results loading them in batch. In GUS 3.5 the name of this
plugin is GUS::Community::Plugin::LoadBatchArrayResults.

---

On Wed, 14 Dec 2005, Sucheta Tripathy wrote:

> Hi Elisabetta,
>
> I am using arrayresultloader to upload the array data into GUS. It does a 
> decent job but crashes inbetween without giving a proper error message. 
> Could it be due to my computer related issues.
>
> Also when I have a line having data such as:
>
> x_position, y_position, mean,       stdv,       npixels,       name, 
> detection,      detection_p_value,    signal
> 621            275           76.0           10.5       25 
> PsAffx.C17000127_at   A                 0.111572                  10.95974
>
> But when I upload the data it changes the fields into:
>
> Debug   621    275    44.0    7.5    25    PsAffx.C17000127_at       A 
> 0.24
> 6094      10.821429
>
> and says mean 44.0 and stdv 7.5 etc.
>
> Is there a reason why the values are changed?
>
> Thanks
>
> Sucheta
>
>
>
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