Question: R code for cn.mops -- if a chromosome does not have CNV ?
gravatar for Bogdan
9 months ago by
Palo Alto, CA, USA
Bogdan470 wrote:

Dear Gunter,

please if I may add another 1-2 questions : after running cn.MOPS per chromosome on a PBS computer cluster, sometimes, in the output it says :

"No CNVs detected. Try changing "normalization", "priorImpact" or "thresholds".
Error in calcIntegerCopyNumbers(ref_analysis_norm0) :
  No CNV regions in result object. Rerun cn.mops with different parameters!
Calls: calcIntegerCopyNumbers -> calcIntegerCopyNumbers"

and of course, that is fine, as we do not aim to identify CNV on each chromosome ;) However, please could you advise :

-- is there a way to print a message when there are no detected CNV instead of receiving the message "Error in calcIntegerCopyNumbers(ref_analysis_norm0) : " , as it would help our pipeline

-- in the message it says "Try changing "normalization", "priorImpact" or "thresholds".". Shall we change any of these parameters though ?

thanks a lot !





ADD COMMENTlink modified 6 months ago by Günter Klambauer480 • written 9 months ago by Bogdan470
gravatar for Günter Klambauer
6 months ago by
Günter Klambauer480 wrote:

Hello again,

And apologies, again, I had not seen your message until now. I see that the error is problematic for your pipeline  - you can try to catch the error using "try()". However, I will change the behaviour from "error" to "warning" in the next version of cn.mops.

You don't need to change your parameters, if you have already adjusted them and they perform well.



ADD COMMENTlink written 6 months ago by Günter Klambauer480
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