copy numbers?
Thank you,
On Tuesday, June 20, 2017 at 10:33:36 PM UTC+1, Emanuel Gonçalves wrote:
>
> Hi Henrik,
>
> There's no direct way of doing this, but as a start you can read in
>> all the writeRegions()-exported segment data for all samples in a data
>> set
there are more '-1's than '0's, again showing there is a skew to negative
ratios.
Am I missing any preprocessing that is required besides the doCRMAv2?
Thank you for your help,
On Wednesday, June 21, 2017 at 5:15:20 AM UTC+1, Henrik Bengtsson wrote:
>
> Ah, my bad - you're correct.
>
>
Hi Henrik,
There's no direct way of doing this, but as a start you can read in
> all the writeRegions()-exported segment data for all samples in a data
> set as explained in
> http://www.aroma-project.org/vignettes/NonPairedCBS/. That will give
> you a data.frame.
>
But that would get me
Hi,
This seems to be working well, although I'm concerned with the raw counts
> distributions of some cell lines as they look skewed to negative values
> (histogram attached, apologises for the poor quality).
>
> Actually, I have seen this effect also using as reference the average of a
>
Dear all,
I'm processing a set of ~200 SNP6 .cel files and then performing
segmentation with CBS. But I would like to know how to extract the data
points data-frame that is used as input to DNAcopy CBS.
The code is as below:
# install.packages('aroma.affymetrix',
Hi all,
I'm processing a large set of SNP6 samples (1020) and performing CBS
segmentations afterwards. It's a very lengthy process and the annoying part
is that it systematically crashes on the last sample, see code and output
below:
# Run CBS paired segmentation with pooled normal samples
ing without re-calling the fit function from CbsModel?
Thanks a lot,
> Then you can get to traceback() a bit sooner.
>
> /Henrik
>
> PS. I assume that you already know that rerunning the commands will
> not redo the actual analysis; already processed samples will be
e an alternative way to export the regions without running the
CbsModel again? I have the previous script running (where only the last
sample was ran in CbsModel) and it seems to be exporting all the processed
samples.
Thanks a bunch,
>
> /Henrik
>
> On Thu, Aug 31, 2017 at 2:42 P
