[BioC] xval in MLInterfaces package

[Martin Morgan]

Xiwei --

The intention was probably that 'group' could be missing, but the way
the code is currently written you will need to specify
group=as.integer(0) if you want to give additional parameters to
knnB. 'L00' is still used as the method of cross-validation, unless a
different 'xvalMethod' is specified. Hopefully this will be fixed in
the next release of Bioconductor.

Martin

"Wu, Xiwei" <XWu at coh.org> writes:

> Marin,
>
> Thank you very much for your hint. It seems to be working as far as the
> group parameter is defined. Otherwise, it will ignore the k parameter. I
> thought group parameter is not necessary if "LOO" is specified. See
> below:
>
>> lk1 <- xval(smallG, "ALL.AML", knnB, xvalMethod = "LOO", k=1)
>> table(given=smallG$ALL.AML, predicted=lk1)
>      predicted
> given ALL AML
>   ALL  37  10
>   AML  10  15
>> lk1 <- xval(smallG, "ALL.AML", knnB, xvalMethod = "LOO",k=2)
>> table(given=smallG$ALL.AML, predicted=lk1)
>      predicted
> given ALL AML
>   ALL  37  10
>   AML  10  15
>> lk1 <- xval(smallG, "ALL.AML", knnB, xvalMethod =
> "LOO",group=as.integer(0), k=1)
>> table(given=smallG$ALL.AML, predicted=lk1)
>      predicted
> given ALL AML
>   ALL  37  10
>   AML  10  15
>> lk1 <- xval(smallG, "ALL.AML", knnB, xvalMethod =
> "LOO",group=as.integer(0), k=2)
>> table(given=smallG$ALL.AML, predicted=lk1)
>      predicted
> given ALL AML
>   ALL  34  13
>   AML   9  16
>
> Xiwei
> -----Original Message-----
> From: Martin Morgan [mailto:mtmorgan at fhcrc.org] 
> Sent: Tuesday, June 27, 2006 4:39 PM
> To: Wu, Xiwei
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] xval in MLInterfaces package
>
> Yes, knnB is invoked with default parameters, and does leave-one-out
> cross-validation. Adding k and l as named arguments (e.g, k=2) to xval
> should change the values of these parameters in knnB.
>
> lk1 <- xval(smallG, "ALL.AML", knnB, xvalMethod = "LOO",
> 	group = as.integer(0), k=2)
>
> Does this work for you?
>
> Martin
>
> "Wu, Xiwei" <XWu at coh.org> writes:
>
>> Hi, all,
>>
>> I am testing the xval() function under MLInterfaces package following 
>> the documentation.
>>
>>> lk1 <- xval(smallG, "ALL.AML", knnB, xvalMethod="LOO",
>> group=as.integer(0))
>>
>> I am wondering when I invoke above, is knnB being invoked with the 
>> default set of parameters to do Leave-One-Out cross validation? If so,
>
>> is it possible to specify my own parameters, such as k and l?
>>
>> Thanks in advance.
>>
>> Xiwei Wu, MD, PhD
>> Director, Affymetrix Core Facility
>> Assistant Research Scientist
>> Department of Biomedical Informatics
>> Beckman Research Institute
>> City of Hope National Medical Center
>> Duarte, CA 91010
>> Phone: (626) 359-8111 ext. 65071
>>
>> "EMF <COH.org>" made the following annotations.
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