Hi,
I've been running SC3 for a few of my singlecellexperiment samples. For many of them it works, but for a few I get a lot of suppressed warning messages and SC3 fails to assign clusters for many of the cells. For example 

sce$sc3_2_clusters produces:  

 [1] 2    <NA> 2    2    2    <NA> 2    2    <NA> <NA> 2    2    2    2    2    <NA> 2    <NA> <NA> 2    <NA> 1    1    2    2    2    1    2    2    2    2    <NA>
  [33] 2    2    2    2    2    2    <NA> 2    1    2    2    2    2    2    <NA> 2    <NA> 2    1    2    2    2    2    2    2    2    2    2    <NA> 1    2    2   
  [65] 2    2    <NA> <NA> 2    2    <NA> 2    2    2    1    2    2    2    1    <NA> <NA> 2    2    1    <NA> 2    <NA> 2    2    2    <NA> 1    2    2    2    2   
  [97] <NA> 2    2    2    2    2    2    <NA> 2    <NA> 2    2    2    <NA> 2    2    <NA> 2    1    2    1    <NA> 2    2    2    <NA> 2    2    2    2    1    2   
 [129] 2    <NA> 1    2    2    2    1    2    2    1    2    1    2    2    2    1    2    <NA> 2    ....

Any ideas? Thanks, James

Hi James, I am afraid I will need your data to be able to reproduce. If you are happy to share it, could you please send it to vk6@sanger.ac.uk in addition with your script and sessionInfo()?