Dear Henrik,
I was trying to run CBS model on a set of paired CN estimates. The
data were generated using an Illumina platform, so I have followed
"Vignette: Creating binary data files containing copy number
estimates" to create the log2ratio CN estimates between a tumor sample
and its matched normal.
I have loaded the data with the following codes:
dataSet = "Dataset,tagA,tagB";
chipType = "HumanOmni1-Quad";
ds = AromaUnitTotalCnBinarySet$byName(dataSet,chipType=chipType);
cbs = CbsModel(ds);
However, when I looked at how the CBS model was set up, it says:
> cbs
CbsModel:
Name: Dataset
Tags: tagA,tagB
Chip type (virtual): HumanOmni1-Quad
Path: cbsData/Dataset,tagA,tagB/HumanOmni1-Quad
Number of chip types: 1
Sample & reference file pairs:
Chip type #1 of 1 ('HumanOmni1-Quad'):
Sample data set:
AromaUnitTotalCnBinarySet:
Name: Dataset
Tags: tagA,tagB
Full name: Dataset,tagA,tagB
Number of files: 10
Names: sample1, sample2, ..., sample10 [10]
Path (to the first file): rawCnData/Dataset,tagA,tagB/HumanOmni1-Quad
Total file size: 43.46 MB
RAM: 0.02MB
Reference data set/file:
<average across arrays>
RAM: 0.00MB
It seems to me that the CBS model is using "<average across arrays>"
as reference, which would not be what I want, since my CN estimates
have already been referenced. So my questions are:
1. Is this how CBS will behave?
2. Is there a way to let CBS take the CN estimates "as is", without
contrasting to any reference?
Thank you very much for your help on this.
Best,
Kai
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
