Opened 9 years ago

Last modified 9 years ago

#211 new Request

Request: R/G quantile normalization

Reported by: jari Owned by: martin
Priority: major Milestone: ZZ A wish list
Component: net.sf.basedb.normalizers Keywords:
Cc:

Description

Copied from the BASE users mailing list (April 27, 2009):

Yannick Lippi wrote:

SECOND QUESTION: R/G quantile normalization

Jari said: Obviously R-G quantile is not supported since the methods in net.sf.basedb.normalizers only work on ratios.

  • i am not expert on java developping.. but what does mean: methods in

net.sf.basedb.normalizers only work on ratios

Yes, the released normalizers work on ratios for 2-channel data. The normalizers work on 1-channel data also but obviously no on ratios in this case. The same is true for the new normalizers in development (to be relased in 1.1 due soon).

  • Do you mean it is not possible to implement plugins to perform R/G

quantile normalizations?

Of course, it is possible to implement such plug-ins. However, there is no plan from our side to do that. As always, we are happy to include contributions from other developers.

  • how could i pass through this problem?

You need to create a plug-in that performs your specific normalization. It should be straightforward to add to the qQuantileNormalizer as options but unfortunately we cannot promise to do this work for you. I'll add R/G qQuantileNormalizations as wish list tickets to the plug-in dev site.

Cheers,

Jari

Change History (1)

comment:1 Changed 9 years ago by jari

  • Type changed from task to Request
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