Re: [aroma.affymetrix] Create binary data files containing BAF data

2012-01-31 Thread Henrik Bengtsson
On Mon, Jan 30, 2012 at 9:45 PM, Kai wangz...@gmail.com wrote: Hi Henrik, Thanks for the detailed explanations. They make a lot of sense. I just had one follow-up question on the format of data stored in an AromaUnitTotalCnBinaryFile when the log2ratio tag is not supplied. In your response,

Re: [aroma.affymetrix] Create binary data files containing BAF data

2012-01-30 Thread Kai
Hi Henrik, Thanks for the detailed explanations. They make a lot of sense. I just had one follow-up question on the format of data stored in an AromaUnitTotalCnBinaryFile when the log2ratio tag is not supplied. In your response, you mentioned that it holds CN ratios on the intensity scale,

Re: [aroma.affymetrix] Create binary data files containing BAF data

2012-01-20 Thread Henrik Bengtsson
Hi. On Thursday, January 19, 2012, Kai wrote: Hi Henrik, In the vignette http://www.aroma-project.org/node/88;, the LRR data were stored under rawCnData, but it seems to me that in recent updates you have created a new sub-directory called totalAndFracBData - what are the difference

Re: [aroma.affymetrix] Create binary data files containing BAF data

2012-01-19 Thread Kai
Hi Henrik, In the vignette http://www.aroma-project.org/node/88;, the LRR data were stored under rawCnData, but it seems to me that in recent updates you have created a new sub-directory called totalAndFracBData - what are the difference between these two directories? Which one should I use?

Re: [aroma.affymetrix] Create binary data files containing BAF data

2012-01-12 Thread Henrik Bengtsson
Yes, the process is basically the same; replace AromaUnitTotalCnBinaryFile with AromaUnitFracBCnBinaryFile. Put the TCN and the BAF data files in the same directory. The BAF files should have the same name as the TCN files but with an *,fracB.asb suffix. The use of AromaUnitFracBCnBinaryFile is