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rietho / IPO

A Tool for automated Optimization of XCMS Parameters
http://bioconductor.org/packages/IPO/
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Allow to select the retcor() method #8

Closed sneumann closed 9 years ago

sneumann commented 9 years ago

Hi, the retcor(method="loess") has quite a performance benefit over the method="obiwarp", so it would be cool if that could be optimised as well. The downside is that this requires method-dependent getDefaultRetGroupStartingParams().

Also, obiwarp is independent of the grouping, while loess depends on reasonable grouping. If oscillation of optimal parameters occurs, that could be a reason. Yours, Steffen

glibiseller commented 9 years ago

Hi Steffen!

It sure would be benefical if IPO supports all XCMS-methods. I think this enhancement and the enhancement issue 5 can be done together. I hope i can start to work on it next week.

best regards

glibiseller commented 9 years ago

Hi Steffen!

Do you have a suggestion for the minimum value for the parameter "span" of the method retcor.loess. Is zero fine or should it be 0.001.

Yours, Gunnar

glibiseller commented 9 years ago

Implemented in version 1.7.0