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
> batc
Hi Henrik,
Perfect with your help I putted together a script that seems capable of
extracting the raw counts (over a pooled reference):
# - Imports
library("Biobase")
library("aroma.affymetrix")
# - Reduce decimal places to minimize space
options(digits=4)
# - Load data
gsT <- doCRMAv2("cancer
Ah, my bad - you're correct.
On Tue, Jun 20, 2017 at 4:40 PM, Emanuel Gonçalves
wrote:
> I think what I'm looking for is:
>
>> extractRawCopyNumbers(cbsmodel, array=1, chromosome=2)
>
>
> Problem is I have ~200 and the function seems to be taking quite sometime to
> get me the results (is this be
I think what I'm looking for is:
extractRawCopyNumbers(cbsmodel, array=1, chromosome=2)
Problem is I have ~200 and the function seems to be taking quite sometime
to get me the results (is this because I don't have all the cbs computed
yet?), is there a way to export the whole data-set raw copy
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 th
Hi.
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.
>From there you should be able to manipulate t
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', repos='http://cran.us.r-projec
