Re: [base] Réplicates in base 2

Thu, 14 Dec 2006 01:22:18 -0800

Nicklas Nordborg a écrit : 
Emmanuel Courcelle wrote:
  
Hello

We are trying to create an experiment composed with:

-4 slides
-3 times each reporter on each slide

So, we have up to 12 replicates for each reporter (sometimes less 
because some flagged spots were filtered out).
How to make a final bioassay set with 6158 averaged-spots instead of 
more than 77000 ?
    


There is no merge plugin available for BASE2. You can try using the 
BASE1 merge plugin which can be found on: 
http://lev.thep.lu.se/trac/baseplugins/wiki/PluginDownload
OK
So I tried the followng:

-download  the Merge BioAssay plugin
-Install file inside some directory (/usr/local/base2/plugins)
-Upload mergebioassay.base to my base's home directory
-Create a configuration for Base1PluginExecuter
-Enter /my_home/mergebioassay.base in the field: File
-Enter /usr/local/base2/plugins in the filed: Plugin executables path

-Go to the bioassay Set
-Click the last set (called Filetered Normalized Mediane)
-Run the plugin

Here what I got (copy-and-paster from the screen, because the export does not show everything):


1       Formula intensity calculator
2   80640 6229  
3       JEP filter plugin
4   77148 6158  
5       Normalization: Median ratio
6   77148 6158  
7       Base1PluginExecuter
8   77148 0  
9

Looks buggy, doesn't it ? did I miss something ?


-- 
Emmanuel COURCELLE                [EMAIL PROTECTED]
L.I.P.M. (UMR CNRS-INRA 2594/441) tel (33) 5-61-28-54-50
B.P.52627 - 31326 CASTANET TOLOSAN Cedex - FRANCE
------


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