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 !