Problems running Nearest Template Prediction (NTP)

[Laura]

I have a problem running NTP, I tried with all the versions available on GenePattern (also version 3 that seems to be the stable one) and it always gives me that all samples belong to class 0. I followed all the instructions for the preparation of the input file.

Job ID 1671913.NearestTemplatePrediction

Thanks 

Laura

[Barbara Hill]

Hello Laura, 

My apologies for the delay in responding. 

I was unable to determine the issue on my own and requested that another colleague take a look. He said that his " hunch is that the combination of log2 normalized data and cosine similarity may be what's leading to predicting all samples to be in the same class", but he didn't have a chance to test that out.

Let us know if that helps get you pointed in the right direction.

Best

-Barbara