Question: PureCN.R warning "duplicate keys in header will be forced to unique rownames"
0
gravatar for twtoal
4 months ago by
twtoal0
twtoal0 wrote:

Running PureCN.R v 1.13.21, I get this warning and these "null device" messages. Are they something to be concerned about?

...snip...
INFO [2019-04-29 15:42:06] Fitting variants for purity 0.37, tumor ploidy 3.73 and contamination 0.01.
Warning message:
In .bcfHeaderAsSimpleList(header) :
  duplicate keys in header will be forced to unique rownames
INFO [2019-04-29 15:42:06] Fitting variants for purity 0.42, tumor ploidy 3.26 and contamination 0.01.
INFO [2019-04-29 15:42:07] Fitting variants for purity 0.37, tumor ploidy 4.13 and contamination 0.01.
INFO [2019-04-29 15:42:07] Fitting variants for purity 0.35, tumor ploidy 1.93 and contamination 0.01.
null device 
          1 
INFO [2019-04-29 15:42:08] Poor goodness-of-fit (0.524). Skipping post-optimization.
INFO [2019-04-29 15:42:08] Optimized purity: 0.62
INFO [2019-04-29 15:42:08] Fitting variants for local optimum 10/15...
null device 
          1 
INFO [2019-04-29 15:42:08] Fitting variants for purity 0.28, tumor ploidy 4.46 and contamination 0.01.
INFO [2019-04-29 15:42:08] Fitting variants for purity 0.74, tumor ploidy 3.00 and contamination 0.01.
null device 
          1 
INFO [2019-04-29 15:42:10] Rare karyotype solution. Skipping post-optimization.
INFO [2019-04-29 15:42:10] Optimized purity: 0.37
INFO [2019-04-29 15:42:10] Fitting variants for local optimum 6/21...
Finished job 17227.
purecn • 108 views
ADD COMMENTlink modified 4 months ago by markus.riester110 • written 4 months ago by twtoal0
Answer: PureCN.R warning "duplicate keys in header will be forced to unique rownames"
0
gravatar for markus.riester
4 months ago by
markus.riester110 wrote:

No, these should be benign. I'll hide these after the next Bioconductor release next week.

ADD COMMENTlink written 4 months ago by markus.riester110
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 149 users visited in the last hour