Re: [base] Formula/plugins

[Irina 264]

Hi Jari,
 
Thanks, I am going to the plugins development 

 
 Date: Fri, 26 Nov 2010 15:53:41 +0100
 From: j...@thep.lu.se
 To: basedb-users@lists.sourceforge.net
 Subject: Re: [base] Formula/plugins
 
 Hi Irina,
 
 There is an average and a quantile normalizer plug-in at 
 http://baseplugins.thep.lu.se/wiki/net.sf.basedb.normalizers
 
 In general one needs plug-ins to mix information between bioassays so a 
 BASE Formula will not do.
 
 
 Hope this helps,
 
 Jari
 
 
 On 2010-11-25 04.39, Irina 264 wrote:
 
  Dear team,
 
  I used plugins and created Formulas for dataset analysis and its work only 
  with each dataset (bioassay) separately; the result is column (Ch1).
  Is it possible to make analysis (for example quantile normalization of 3 
  bioassays, or formula to find mean between bioassay1 (Ch1))and bioassay2 
  (Ch1)).
  When i used 3 bioassays for normalization i have result again only one 
  column Ch1 but 3 times longer and analysis was done for each bioassay 
  separately.
  Did I missed something or I have to develop plugin to operate between 
  bioassays?
 
  Regards,
  Irina
  
 
 
 
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Re: [base] Formula/plugins

[Nicklas Nordborg]

On 2010-11-25 04:39, Irina 264 wrote:
 Dear team,


 I used plugins and created Formulas for dataset analysis and its work
 only with each dataset (bioassay) separately;

What do you mean with this? What plug-in did you use? What are the formulas?

  the result is column
 (Ch1). Is it possible to make analysis (for example quantile
 normalization of 3 bioassays, or formula to find mean between
 bioassay1 (Ch1))and bioassay2 (Ch1)). When i used 3 bioassays for
 normalization i have result again only one column Ch1 but 3 times
 longer and analysis was done for each bioassay separately. Did I
 missed something or I have to develop plugin to operate between
 bioassays?


I am not sure I understand what you have done and what you want to do. 
Can you please explain in more detail? The Lowess and median-ratio 
normalization that is shipped with BASE only works with 2-channel data 
so I am not sure which plug-in you have used.

/Nicklas

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