Question: Failure to cluster SC3
0
gravatar for jhopkins
13 months ago by
jhopkins0
jhopkins0 wrote:

 

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

 

sc3 • 261 views
ADD COMMENTlink modified 13 months ago by Vladimir Kiselev150 • written 13 months ago by jhopkins0
Answer: Failure to cluster SC3
0
gravatar for Vladimir Kiselev
13 months ago by
Sanger Institute, Cambridge, UK
Vladimir Kiselev150 wrote:

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()?

ADD COMMENTlink written 13 months ago by Vladimir Kiselev150
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