Hi, I am trying to do some CGH analysis on an external dataset and I am using snapCGH as the frontend to the CGH functions. I have been getting some warning messages and I would like to know whether I should be concerned about these or not. After running processCGH() I get the following: collapsing to unique 'x' values in: approx(lowess(kbl[ind], vecl[ind], f = smooth), xout = kbl[-ind]) And after running runDNAcopy() I get: Warning message: array has repeated maploc positions in: CNA(log2ratios(input), input$genes$Chr, input$genes$Position, The strange thing is that I have used processCGH to average when there are the same Clone ID, so I would have though duplicate locations would be removed. Many Thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addre...{{dropped}}

Daniel Brewer <daniel.brewer at="" ...=""> writes: > > After running processCGH() I get the following: > collapsing to unique 'x' values in: approx(lowess(kbl[ind], vecl[ind], f > = smooth), xout = kbl[-ind]) Dan, Don't know the answer - just a possible stab in the dark. Errors in processCGH like the ones you are getting might be caused by too few observations (too many NAs) in the MA data. You could try either (1) impute missing values, or (2) cut down on the number of autosomes you process to see if one particular chromosome is misbehaving. I get a similar error in aCGH package if I include Chr 22 in my analysis - not enough data points. > > And after running runDNAcopy() I get: > Warning message: > array has repeated maploc positions I get the exact same error ... re:DNAcopy, but BioHMM and GLAD all work fine let me know if you uncover the answer. Best wishes, Ian