Hi Henrik,
Thank you for letting me know the hidden trick. It seems to work. I
have another related question regarding the CbsModel function.
You've mentioned in addressing another post that for non-affy
platforms, once one has setup a platform-independent data set (*.asb
files) as in Vignette: Creating binary data files containing copy
number estimates, e.g.
ds - AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags,
chipType=*);
One can then pass this to CbsModel just as one passes an
CnChipEffectSet 'ces' in other vignettes for affymetrix genotyping
platforms. However, it seems to me that what are stored in the
CnChipEffectSet are raw CN estimates, whereas the
AromaUnitTotalCnBinaryFile objects contain log2 CN ratios.
If these are correct, my question is that how CbsModel can tell
whether the input data are in log2-scale or not, or whether the input
data are ratios or not? Thank you very much for your help on this.
Best,
Kai
On Sep 20, 1:06 pm, Henrik Bengtsson h...@aroma-project.org wrote:
Hi Kai.
I am aware of the issue, and it is on the todo list to add argument
specify that you don't want ratios to be calculated. There is
currently a secret workaround for this that should not be read as an
official documented feature [that's a warning for users reading this
thread in the future], but it should solve your immediate needs.
cbs - CbsModel(ds);
cbs$.calculateRatios - FALSE;
See if that does it for you.
/Henrik
On Wed, Sep 15, 2010 at 10:14 PM, Kai wangz...@gmail.com wrote:
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
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