Hi. On Wed, Sep 22, 2010 at 9:35 AM, Kai <wangz...@gmail.com> wrote: > 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$byName(dataSet, tags=tags, > chipType="*"); > > One can then pass this to CbsModel just as one passes an > CnChipEffectSet 'ces' in other vignettes for affymetrix genotyping > platforms. However, it seems to me that what are stored in the > CnChipEffectSet are raw CN estimates, whereas the > "AromaUnitTotalCnBinaryFile" objects contain log2 CN ratios. > > If these are correct, my question is that how CbsModel can tell > whether the input data are in log2-scale or not, or whether the input > data are ratios or not? Thank you very much for your help on this.
It does this by looking for special tags of the *.asb file. More precisely, if the filename has a "log2ratio" tag, then it's content is assumed to log2-ratio. Likewise, if there is a "log10ratio" tag, it's content is assumed to be log10-ratios. For historical reasons, a "logRatio" tag is interpreted as "log10ratio". If none of these tags exist, the content is assumed to be on the non-logarithmic scale. I recommend to use non-logged storage, because that is well defined also for non-positive values. DETAILS: The above is taken care of by the AromaUnitTotalCnBinaryFile class and more precisely the internal/private getAM() method. The CbsModel and likewise does not know about this layer and happily receives log2 ratios regardless of what is stored on file. Hope this helps /Henrik > > Best, > Kai > > > > On Sep 20, 1:06 pm, Henrik Bengtsson <h...@aroma-project.org> wrote: >> Hi Kai. >> >> I am aware of the issue, and it is on the todo list to add argument >> specify that you don't want ratios to be calculated. There is >> currently a secret workaround for this that should not be read as an >> official documented feature [that's a warning for users reading this >> thread in the future], but it should solve your immediate needs. >> >> cbs <- CbsModel(ds); >> cbs$.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/ > -- 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/