Github user VinceShieh commented on a diff in the pull request:

    https://github.com/apache/spark/pull/14858#discussion_r77465278
  
    --- Diff: 
mllib/src/main/scala/org/apache/spark/ml/feature/QuantileDiscretizer.scala ---
    @@ -114,10 +115,10 @@ final class QuantileDiscretizer @Since("1.6.0") 
(@Since("1.6.0") override val ui
         splits(0) = Double.NegativeInfinity
         splits(splits.length - 1) = Double.PositiveInfinity
     
    -    val distinctSplits = splits.distinct
    +    val distinctSplits = splits.filter(!_.isNaN).distinct
    --- End diff --
    
    @srowen  then maybe we should, as we discussed earlier on JIRA, align with 
R, by having a NaN checker in approxQuantile, that is, having a NaN filter 
inside of approxQuantile, rather than ahead of calling approxQuantile.
    
    We can also have a same flag for user to choose to either remove NaN values 
or throw an error when there is NaN in data,  although, this API change will 
introduce collateral impact on several existing function calls. 


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