aCGH
0
0
Entering edit mode
@sean-davis-490
Last seen 3 months ago
United States
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
aCGH CGH impute aCGH aCGH CGH impute aCGH • 1.2k views
ADD COMMENT

Login before adding your answer.

Traffic: 633 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6