MINT output BER vs overall is swapped?

[Kim-Anh Le Cao]

It seems to me that the numerical outputs from MINT should be swapped (BER/overall), see the stemcells case study http://mixomics.org/mixmint/stemcells-example/ (code are on bitbucket in Wordpress/) and screenshot attached

Could you double check, and also check for the other methods output? Thanks Florian!! Screen Shot 2018-05-18 at 10.43.10 am.png

[Florian Rohart]

BER max.dist is in solid purple line: comp1 0.51, comp2 0.37

overall max.dist in is dotted purple line: comp1 0.56, comp2 0.41

dotted purple line higher than solid purple line, which is what we see in the graph. no?

[Kim-Anh Le Cao]

I was thinking more about the output in general. I was surprised to see that the BER < overall error rate. I had a user recalculating the weighted error rates and maybe the numbers have been swapped (i.e. BER should be 0.568 on comp 1 max dist instead of 0.51289).

[Florian Rohart]

Well, I don't know how that user calculated BER and overall errors, but the code checks out:

            conf = get.confusion_matrix(truth = factor(Y), predicted = x)
            BER = get.BER(conf)
            overall = sum(apply(conf, 1, sum) - diag(conf)) / length(Y)

[Kim-Anh Le Cao]

Alright thanks, closing this issue now