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
>
> > --
> > 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 websitehttp://www.aroma-project.org/.
> > To post to this group, send email to aroma-affymetrix@googlegroups.com
> > To unsubscribe and other options, go tohttp://www.aroma-project.org/forum/
--
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/
