Hi.
On Thu, Jun 18, 2009 at 12:00 PM, han wrote:
>
> Hi Henrik:
>
> Thanks for the help, I think that I found out why. I guess that
> names of Nsp and Sty CEL files must be the same except the "Nsp/Sty"
> part. Can "Nsp/Sty" appear any part in the file name?
This is documented in the vignett
Hi.
On Thu, Jun 18, 2009 at 9:44 AM, han wrote:
>
> Hi Henrik:
>
> I am looking at SNP 500K data for cell-lines that was released from
> GSK.
Are you referring to the 'GSK Cancer Cell Line Genomic Profiling Data'
data set listed on:
http://groups.google.com/group/aroma-affymetrix/web/data-sets?
Hi Henrik:
Thanks for the help, I think that I found out why. I guess that
names of Nsp and Sty CEL files must be the same except the "Nsp/Sty"
part. Can "Nsp/Sty" appear any part in the file name?
By the way, what are the two dotted lines below and above the zero
line. I guess that there ar
Hi Henrik:
I am looking at SNP 500K data for cell-lines that was released from
GSK. I followed your example CRMA v2. with CBS segmentation without
reference samples. It seems that the scale/dynamic range in the plus
side (amplification) is compressed compared with similar data from
other sourc
Hi,
are you saying you do not get results from any chromosome? If so,
that's a first very useful clue; if you get from some, something odd
is going odd. Doing CN analysis on these chips is standard procedure,
so it "should work" out of the box.
In order to help you, what version are you using,
Dear Henrik:
I am processing 500k data for cell-lines, following your CRMA2
example, then using CBS for seqgmentation "cbs <- CbsdModel
(cesNList)"; than used ChromosomeExplorer to dsiplay, and used
"getRegions" to get segment infomation.
My question is how can I get combined Nsp+Sty plots and s
See earlier CRMA (v1) vignette 'Total copy number analysis (10K, 100K, 500K)'
http://groups.google.com/group/aroma-affymetrix/web/total-copy-number-analysis
on how these are combined in the segmentation step after being
preprocessed separately.
/Henrik
On Thu, Jun 18, 2009 at 8:53 AM, han wrot
Hi,
update aroma.affymetrix et al. and retry.
/Henrik
On Thu, Jun 18, 2009 at 5:01 AM,
cstratowa wrote:
>
> Dear all,
>
> Below I show you the relevant code fragments of my function "computeCN
> ()" to compute copy-number regions using model CBS. This function can
> compute copy-number regions
Dear all,
Below I show you the relevant code fragments of my function "computeCN
()" to compute copy-number regions using model CBS. This function can
compute copy-number regions for the usual case (reference=NULL), for
pairs of samples (reference="Pairs") or using reference samples
(reference="R
