Hi Oscar,
I'm rather swamped right now, but just a few quick comments. Calling
so called copy-neutral segments via callNTCN() is a rather and
somewhat experimental method (I should state in the vignette). In
other words, it has not undergone equally much rigorous validation as
the other callers.
Hi Henrik,
That works, but with another sample, trying the last step suggested in the
vignette I get another error:
> fit <- callLOH(fit, verbose = -10)
> deltaCN <- estimateDeltaCN(fit, scale=1)
> fit <- callNTCN(fit, delta=deltaCN, verbose=-10)
..
Identifying segments that are co
On Wed, Oct 26, 2011 at 5:11 PM, Ivan Smirnov wrote:
> Thanks Henrik, you nailed it! It was a matter of the wrong version of
> UFL file. Why did you post those other non-Full versions anyway?
> Aren't we always supposed to use only Full version of GenomeWideSNP_6
> CDF?
Yes, but for completeness
Thanks Henrik, you nailed it! It was a matter of the wrong version of
UFL file. Why did you post those other non-Full versions anyway?
Aren't we always supposed to use only Full version of GenomeWideSNP_6
CDF?
Ivan
On Wed, Oct 26, 2011 at 2:36 AM, wrote:
> Today's Topic Summary
>
> Group: http
Hi.
On Tue, Oct 25, 2011 at 9:22 AM, Ivan Smirnov wrote:
> Hi Pierre, thanks for prompt reply, however I do have all those
> annotation files downloaded from that link, see below. Do I need to
> rename them (e.g. remove tags)?
>
> /aroma.exon: ls -l annotationData/chipTypes/GenomeWideSNP_6
> tota
Hi Pierre, thanks for prompt reply, however I do have all those
annotation files downloaded from that link, see below. Do I need to
rename them (e.g. remove tags)?
/aroma.exon: ls -l annotationData/chipTypes/GenomeWideSNP_6
total 1099456
-rw-r--r-- 1 ivan ivan 493291745 2011-10-23 20:03 GenomeWide
