>From trial and error I see I can simply use the function:
AromaUnitTotalCnBinarySet()
and pass it my list of files.
On Mar 9, 11:32 am, Gregory W wrote:
> Hello,
>
> Simple question I'm sure but I can't seem to find the solution on the
> forum or d
Hello,
Simple question I'm sure but I can't seem to find the solution on the
forum or docs.
I have a list of AromaUnitTotalCnBinaryFiles.
Can someone tell me how I can convert this to a single
AromaUnitTotalCnBinarySet?
Many thanks,
Greg
--
When reporting problems on aroma.affymetrix, make su
Hello,
Many thanks for the site and quick feedback to the discussion board.
I was hoping to get a little clarification about the difference
between these two statistics: Raw CN and CBS mean.
After running CBS I get the following data frame:
cbs <- CbsModel(tumor, normal, min.width=5, alpha = .
Thanks Henrik for the reply.
FYI.
I ran the analysis twice: once using a paired approach and once using
a large global reference group.
Method: CRMAv2 -> CbsModel -> GISTIC
There was approximately 50% agreement between the two results.
I noticed one interesting fact:
Almost ALL regions that w
Hello,
I was hoping to get some information about how to manipulate
AromaUnitTotalCnBinarySets.
I've already performed CRMAv2 on all the affy platforms in my study.
I load the results into an R session with:
>tags <- "ACC,ra,-XY,BPN,-XY,AVG,FLN,-XY" ;
>dsT <- AromaUnitTotalCnBinarySet
Hello,
I was hoping to get some insight as to whether using a pooled
reference or paired normal is more appropriate when performing cbs.
I could see how using a paired tumor normal approach could be
beneficial, say, by negating benign CNVs in the individuals germline.
I believe these germline CNV
Hello,
I've been able to take advantage of CRMAv2 ability to process arrays
in parallel, which is great.
However, when I revisit the data to run, say, CBS on different subsets
of the samples I encounter a very long data load time.
In particular when I open a new R session I basically run the
fol
I should state that I know about the "How tos" section. It seems like
its still under construction.
And
> ?GenomeInformation
gives some helpful suggestions but at times it can be a little
overwhelming with all the inherited classes.
On Dec 29, 12:43 pm, Gregory W wrote:
&
Hello,
I have what I think its a pretty easy question.
After reading in the CDF file and getting basic information:
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
> print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/GenomeWideSNP_6
Filename: GenomeWideSNP_6,Full
Hello,
Thanks for aroma.affymetrix and this helpful site.
I was hoping to get some general advice. I know CRMAv2 is a single
array method and thus makes processing different arrays in parallel
possible.
I was wondering how you would setup the rawData and annotationData
directories when doing mul
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