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?
Regards,
Irina
> Date: Fri, 20 May 2011 07:51:52 +0200
> From: nick...@thep.lu.se
> To: basedb-users@lists.sourceforge.net
> Subject: Re: [base] reporters on MergeBioAssay plug-in
>
> On 2011-05-20 03:46, Irina 264 wrote:
> > Dear team,
> >
> > I am working with MergeBioAssay plug-in. I created a formula for
> > reporterID using rep(‘id’) as expression, because other reporter
> > parameters (Name or ExternalID) don’t work. However, when I run
> > MergeBioAssay with Affy dataset I have an error message:
> >
> > “Error: Raw data for raw data type: Affymetrix is not stored in the
> > database.”
>
> I don't see how this error message can be coming from the Merge BioAssay
> plug-in. Can you explain better what you are doing when you get that
> error message. Eg. which menus, buttons, etc. you click on to get there?
>
> > Could you help me, what is better way to solve it: to add Affy data
> > format to the raw-data-types.xml or you have another idea?
>
> Affymetrix raw data should never be added to the database. There are too
> many data points for this to work satisfactory. You'll have to rely on
> other plug-ins for getting the data into the database. See for example
> http://baseplugins.thep.lu.se/wiki/se.lu.thep.affymetrix
>
> /Nicklas
>
>
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