Entering edit mode
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