On Fri, May 17, 2013 at 3:43 PM, Ryan C. Thompson <rct@thompsonclan.org>wrote:

> I can't see how the output of pamr.listgenes would be sufficient to
> reproduce a trained classifier. I think your only choice would be to re-run
> PAM starting from the CEL files.
>

Thank you, this is why I got so stuck.  The table listed in their paper
that's labeled "classifier" is not actually a classifier.   Do you have any
idea what the list of centroids is used for if not to create a classifier?
Wouldn't it be more useful to publish something like
"pamrtrained.RData.gz", so people can just download it, load the object and
start classifying?



>
> Also, consider whether their classifier would even be applicable to your
> microarray samples, since your samples and theirs are normalized separately.
>

One of the papers I'm working off of (DeSousa 2013, doi:10.1038/nm.3174)
has a flow chart in the supplementary figures that shows how they trained
the classifier from one dataset of 90 patients, and then applied that
classifier to 5 different datasets from several different platforms.  There
are no loops in the flow chart that indicate they retrained the classifier
for each dataset.  Are they doing it wrong, or is this a valid procedure?

I hope DeSousa 2013 is on topic, as they even provided a bioconductor
package to repeat their analysis.  I can use that package to recreate their
classifier pretty easily, but others aren't so convenient.  Thanks a bunch
for the clarification.
-Ed

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