Re: [aroma.affymetrix] Raw copy numbers calculation using common reference instead of average of all samples

2013-08-06 Thread ying chen
I see. Thanks a lot, Sean On Tue, Aug 6, 2013 at 8:05 PM, Henrik Bengtsson < henrik.bengts...@aroma-project.org> wrote: > Hi. > > On Tue, Aug 6, 2013 at 12:31 PM, ying chen wrote: > > Hi Henrik, > > > > > > Sorry I have one more question to bug you. The urls in the df (by df <- > > readDataFra

Re: [aroma.affymetrix] Raw copy numbers calculation using common reference instead of average of all samples

2013-08-06 Thread Henrik Bengtsson
Hi. On Tue, Aug 6, 2013 at 12:31 PM, ying chen wrote: > Hi Henrik, > > > Sorry I have one more question to bug you. The urls in the df (by df <- > readDataFrame(db);) point to UCSCgenome browser with NCBI36/hg18 assembly. I > looked at the http://www.aroma-project.org/chipTypes/GenomeWideSNP_6 pa

Re: [aroma.affymetrix] Raw copy numbers calculation using common reference instead of average of all samples

2013-08-06 Thread ying chen
Hi Henrik, Sorry I have one more question to bug you. The urls in the df (by df <- readDataFrame(db);) point to UCSCgenome browser with NCBI36/hg18 assembly. I looked at the http://www.aroma-project.org/chipTypes/GenomeWideSNP_6 page resource part, the SNP6 chip type files are listed as based on

Re: [aroma.affymetrix] Raw copy numbers calculation using common reference instead of average of all samples

2013-08-02 Thread Henrik Bengtsson
On Thu, Aug 1, 2013 at 6:37 PM, ying chen wrote: > Hi Henrik, > > Thanks a lot for the help. > > For sm <- CbsModel(dsTR, ref=dfR, tags="HapMapRef"), you mean sm <- > CbsModel(dsT, ref=dfR, tags="HapMapRef"), right? Correct, I meant: sm <- CbsModel(dsT, ref=dfR, tags="HapMapRef") /H > > Thanks

Re: [aroma.affymetrix] Raw copy numbers calculation using common reference instead of average of all samples

2013-08-01 Thread ying chen
Hi Henrik, Thanks a lot for the help. For sm <- CbsModel(dsTR, ref=dfR, tags="HapMapRef"), you mean sm <- CbsModel(dsT, ref=dfR, tags="HapMapRef"), right? Thanks, Sean On Thu, Aug 1, 2013 at 6:00 PM, Henrik Bengtsson < henrik.bengts...@aroma-project.org> wrote: > On Mon, Jul 29, 2013 at 7:4

Re: [aroma.affymetrix] Raw copy numbers calculation using common reference instead of average of all samples

2013-08-01 Thread Henrik Bengtsson
On Mon, Jul 29, 2013 at 7:45 PM, ying chen wrote: > Hi Henrik, > Thanks a lot for the help! > Sorry I have more questions. I am following "How to: Calculate total copy > number ratios from total (non-polymorphic) signals" and "Vignette: Total > copy-number segmentation (non-paired CBS)", but I am

Re: [aroma.affymetrix] Raw copy numbers calculation using common reference instead of average of all samples

2013-08-01 Thread ying chen
Sorry, one more question regarding CBS. During fit(sm, verbose=-10) Building tuple of reference sets... Type of reference: median No reference available. Calculating average copy-number signals... Retrieving average unit signals across 291 arrays... .. I tho

Re: [aroma.affymetrix] Raw copy numbers calculation using common reference instead of average of all samples

2013-08-01 Thread ying chen
Sorry, one more question regarding CBS. During fit(sm, verbose=-10) Building tuple of reference sets... Type of reference: median No reference available. Calculating average copy-number signals... Retrieving average unit signals across 291 arrays... .. On Thu, Aug 1, 2013 at 10:53 AM, y

Re: [aroma.affymetrix] Raw copy numbers calculation using common reference instead of average of all samples

2013-08-01 Thread ying chen
Hi Henrik, I tried method I mentioned above. But I got an error message when running fit(sm, verbose=-10). Array #1 ('321T') of 291 on chromosome 1... Error in UseMethod("getChecksum") : no applicable method for 'getChecksum' applied to an object of class "list" What did I do wrong? Than

Re: [aroma.affymetrix] Raw copy numbers calculation using common reference instead of average of all samples

2013-07-29 Thread ying chen
Hi Henrik, Thanks a lot for the help! Sorry I have more questions. I am following "How to: Calculate total copy number ratios from total (non-polymorphic) signals" and "Vignette: Total copy-number segmentation (non-paired CBS)", but I am not sure if I do it correctly. I have two SNP6 datasets Tumor

Re: [aroma.affymetrix] Raw copy numbers calculation using common reference instead of average of all samples

2013-07-28 Thread Henrik Bengtsson
Hi. On Fri, Jul 26, 2013 at 8:02 AM, sean nj wrote: > Hi guys, > > I have a question regarding how to calculate raw copy numbers using common > reference instead of average of all samples of the study. Basically I want > to use average of HapMap270 samples as reference for all further copy number

[aroma.affymetrix] Raw copy numbers calculation using common reference instead of average of all samples

2013-07-26 Thread sean nj
Hi guys, I have a question regarding how to calculate raw copy numbers using common reference instead of average of all samples of the study. Basically I want to use average of HapMap270 samples as reference for all further copy number calculations. I have a bunch HapMap270 snp6 cel files a