Opened 15 years ago
Last modified 15 years ago
#211 new Request
Request: R/G quantile normalization
| Reported by: | Jari Häkkinen | Owned by: | Martin Svensson |
|---|---|---|---|
| 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
