[aroma.affymetrix] Clarification of Raw CN estimates and CBS mean

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 = .

[aroma.affymetrix] Re: Clarification of Raw CN estimates and CBS mean

CORRECTION: ref.theta <- extractMatrix(Normal) theta <- extractMatrix(Tumor) C <- 2 * theta/ref.theta On Mon, Dec 12, 2011 at 1:09 PM, Gregory W wrote: > Hello, > > Many thanks for the site and quick feedback to the discussion board. > > I was hoping to get a little clarification a

Re: [aroma.affymetrix] hg18 annotation files for SNP6

Hi, you'll find old On Thu, Dec 8, 2011 at 12:03 PM, wisekh6 wrote: > Dear Henrik, > I am looking for the old na30 (hg18) annotation files for SNP6 that > are necessary for running CRMA v2. Not sure what you mean by "old [...] that are necessary"; you obviously use the newer ones too. > I don'

Re: [aroma.affymetrix] Re: Clarification of Raw CN estimates and CBS mean

Hi, On Mon, Dec 12, 2011 at 1:15 PM, Greg Wall wrote: > CORRECTION: > > ref.theta <- extractMatrix(Normal) > theta     <- extractMatrix(Tumor) > C         <- 2 * theta/ref.theta > > > On Mon, Dec 12, 2011 at 1:09 PM, Gregory W wrote: >> >> Hello, >> >> Many thanks for the site and quick feedba

Re: [aroma.affymetrix] Combining data from multiple chip types

Hi. On Fri, Dec 9, 2011 at 7:02 PM, Steven McKinney wrote: > Dear Henrik > > Thanks to your instructions, I have set up and run initial processing on my > tumour - normal pairs for copy number analysis.  However I am as yet > unable to determine how to hand off the processed data to CbsModel > or