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Old 09-28-2011, 02:01 PM   #2
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Location: Switzerland

Join Date: Sep 2011
Posts: 1

I assume you have to set the CHASMDIR evironment variable, because I got a similar error when I did not do that, if I remember correctly.
Because I'm going to use CHASM from a script, I add the setting of that variable before the BuildClassifier command. Like this:
CHASMDIR=/opt/CHASM /opt/CHASM/BuildClassifier -m /opt/CHASM/ClassifierPack/contexts/BR.context -i /opt/CHASM/ClassifierPack/calibrate.tmps -o breast_cancer

I also have a question:
Is it the idea to use the "calibrate" set of mutations for building the classifier, like I did in the above command? And then use RunChasm on the mutation-list of cancer samples I want to test?
Or should the model be calibrated on the *same* set of mutations I will use RunChasm on?

Last edited by nyk; 09-28-2011 at 02:08 PM.
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