On Wednesday 29 November 2006 05:26, Jo?o Fadista wrote: > Hi Sean, > > It seems that I have successfully made the log2.ratios and the clones.info > files ready to start analysis with the aCGH package. But I have 2 > questions: > > > 1 - When I use the impute.lowess function it give me some warnings. Do you > know if there is any problem? I put the clones.info and log2.ratios files > in attachment. Changing the argument maxChrom = 23 it gives the same > warnings. > > > log2.ratios.imputed(ex.acgh) <- impute.lowess(ex.acgh, maxChrom = 24) > > Processing chromosome 1 > Processing chromosome 2 > Processing chromosome 3 > Processing chromosome 4 > Processing chromosome 5 > Processing chromosome 6 > Processing chromosome 7 > Processing chromosome 8 > Processing chromosome 9 > Processing chromosome 10 > Processing chromosome 11 > Processing chromosome 12 > Processing chromosome 13 > Processing chromosome 14 > Processing chromosome 15 > Processing chromosome 16 > Processing chromosome 17 > Processing chromosome 18 > Processing chromosome 19 > Processing chromosome 20 > Processing chromosome 21 > Processing chromosome 22 > Processing chromosome 23 > There were 50 or more warnings (use warnings() to see the first 50) > > > warnings() > > Warning messages: > 1: collapsing to unique 'x' values in: approx(lowess(kbl[ind], vecl[ind], f > = smooth), xout = kbl[-ind]) 2: collapsing to unique 'x' values in: > approx(lowess(kbr[ind], vecr[ind], f = smooth), xout = kbr[-ind]) . Do you have multiple probes with the same chromosome locations? I suspect yes. I think these might be responsible for the warnings, but I'm not sure. I would simply plot the non-imputed data and the imputed data to make sure that the imputation is working as you think it should. > 2 - When I plot my acgh object it give me some strange plot comparing to > the examples in the aCGH library. I put also this file in attachment. > Thanks once again. What is "strange" about it? Keep in mind that often CGH segmentation methods need some tuning to get the performance correct for a given dataset. It may be that you need to do that for your data. Sean