Addition, from "Parameters" tab:
Job parameters
-- Ratio annotation type
--- Ratio annotaion value
(ignored unless a Ratio annotation type is selected)
assayname
%1_%2_%3
Child description
Child name
human
Group
%3
Merge method
arithmetric mean or
intensity
newname
Output directory
/home/raw
data/affyExp/MergeBioAssay
- Ratio (ignored if merge
method is other than 'ratio of ratio')
section
merge_bioassays settings
Bioassay set
human
Plugin configuration parameters
Parameter version
27 (27)
Name of executable
run
Plugin executables path
/opt/base2/plugins/MergeBioAssay/
Average on reporters
false
Job parameters
<jobparameters>
<parameter position="1" type="h">
<name>section</name>
<commonname>newname</commonname>
<options>10</options>
<defaultvalue>merge_bioassays settings</defaultvalue>
</parameter>
<parameter position="2" type="t">
<name>assayname</name>
<commonname>assayname</commonname>
<options>10</options>
<defaultvalue>%1</defaultvalue>
</parameter>
<parameter position="3" type="t">
<name>group</name>
<commonname>Group</commonname>
<options>10</options>
<defaultvalue>%1</defaultvalue>
</parameter>
<parameter position="4" type="t">
<name>newname</name>
<commonname>newname</commonname>
<options>10</options>
<defaultvalue />
</parameter>
<parameter position="5" type="e">
<name>mergeMethod</name>
<commonname>Merge method</commonname>
<options>30</options>
<defaultvalue>0</defaultvalue>
<enumoptions>
<value key="0">geometric mean of ratio</value>
<value key="1">arithmetric mean or ratio</value>
<value key="2">arithmetric mean or intensity</value>
<value key="3">ratio of ratio</value>
</enumoptions>
</parameter>
<parameter position="6" type="t">
<name>ratio</name>
<commonname>- Ratio (ignored if merge method is other than 'ratio of
ratio')</commonname>
<options>10</options>
<defaultvalue />
</parameter>
<parameter position="7" type="n">
<name>annType</name>
<commonname>-- Ratio annotation type</commonname>
<options>30</options>
<defaultvalue>0</defaultvalue>
</parameter>
<parameter position="8" type="t">
<name>annValue</name>
<commonname>--- Ratio annotaion value (ignored unless a Ratio annotation
type is selected)</commonname>
<options>10</options>
<defaultvalue />
</parameter>
</jobparameters>
Leave stdin.txt
true
Leave stdout.txt
true
Max channels
2
Min channels
1
Allow override
Resulting intensities
Data format
false
Source intensities
Columns
position\treporter
Fields
intensity1\tintensity2
Version
2.1
> Date: Fri, 20 May 2011 09:21:12 +0200
> From: nick...@thep.lu.se
> To: basedb-users@lists.sourceforge.net
> Subject: Re: [base] reporters on MergeBioAssay plug-in
>
> On 2011-05-20 09:04, Irina 264 wrote:
> > Hi Nicklas,
> >
> > Thanks for the quick reply.
> >
> > I run RMAExpress with Affy data, then I done filtering with equal size
> > of arrays afterwards.
> >
> > Then I run MergeBioAssay (with Base1pluginExecuter) to find average
> > between replicates (grouping assays by control and treatment with method
> > ‘arithmetic mean of intensity) and have this error message: “Error: Raw
> > data for raw data type: Affymetrix is not stored in the database.”
> >
> > When I use Agilent data, i have no problems.
> >
> > Did I explain better?
>
> Yes... but I still have no idea why the error about raw data is coming
> up... As far as I know the Merge BioAssay plug-in doesn't use raw data
> for the calculations. It would be useful to get a complete stacktrace of
> the error in order to locate the source of the problem.
>
> Do you get the error while you are configuring the job? If so you should
> be able to display more error information by clicking on the little [+]
> icon in the configuration wizard.
>
> Or, if you get the error while the plug-in is running, there is a "Stack
> trace" tab in the job dialog.
>
>
> /Nicklas
>
>
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