OK, I figured out a few things myself, but still have some questions about the allelic cross talk calibration.
As mentioned in the Vignette 'Total Copy Number Analysis (5.0 & 6.0)', the tag 'ra' means that all values are rescaled together. I checked the AllelicCrosstalkCalibration() function, the default of 'rescaleBy' is to rescale all cells together, i.e. 'all'. However, I noticed in my case (Affymetrix 500K samples, see my first post here), if I did not specify 'rescaleBy', the default is 'group' rather than 'all': > acc <- AllelicCrosstalkCalibration(csR, model="CRMAv2") > print(acc) ...... Algorithm parameters: (rescaleBy: chr "groups", targetAvg: num [1:2] 2200 2200, subsetToAvg: chr "-XY", mergeShifts: logi TRUE, B: int 1, flavor: chr "sfit", algorithmParameters:List of 3, ..$ alpha: num [1:8] 0.1 0.075 0.05 0.03 0.01 0.0025 0.001 0.0001, ..$ q: num 2, .. $Q: num 98) ...... I also tried to specify 'rescaleBy' as 'all' in CRMAv2: > acc <- AllelicCrosstalkCalibration(csR, rescaleBy="all", model="CRMAv2") It still did not work: > print(acc) ...... Algorithm parameters: (rescaleBy: chr "groups", targetAvg: num [1:2] 2200 2200, subsetToAvg: chr "-XY", mergeShifts: logi TRUE, B: int 1, flavor: chr "sfit", algorithmParameters:List of 3, ..$ alpha: num [1:8] 0.1 0.075 0.05 0.03 0.01 0.0025 0.001 0.0001, ..$ q: num 2, .. $Q: num 98) ...... I guess this has been explained (http://groups.google.com/group/aroma- affymetrix/browse_thread/thread/51a712cf0fabae27#), that if CRMAv2 is specified, the rest parameters can not be changed, and in this case, 'rescaleBy' is set to 'group'. Note we used Affymetrix 500K samples here. I also tested HapMap Affymetrix 5.0 samples and found that the default of 'rescaleBy' is 'all' > acc <- AllelicCrosstalkCalibration(cs, model="CRMAv2") > print(acc) AllelicCrosstalkCalibration: Data set: HapMap_5.0 Input tags: User tags: * Asterisk ('*') tags: ACC,ra,-XY Output tags: ACC,ra,-XY Number of files: 10 (448.26MB) Platform: Affymetrix Chip type: GenomeWideSNP_5,Full,r2 Algorithm parameters: (rescaleBy: chr "all", targetAvg: num 2200, subsetToAvg: chr "-XY", mergeShifts: logi TRUE, B: int 1, flavor: chr "sfit", algorithmParameters:List of 3, ..$ alpha: num [1:8] 0.1 0.075 0.05 0.03 0.01 0.0025 0.001 0.0001, ..$ q: num 2, ..$ Q: num 98) Output path: probeData/HapMap_5.0,ACC,ra,-XY/GenomeWideSNP_5 Is done: FALSE RAM: 0.01MB So it seems that the default of 'rescaleBy' is 'group' for 500K samples and 'all' for 5.0/6.0 samples, which can not be changed in CRMAv2 model. Does using 'group' or 'all' make any big difference in the analysis? Which one is recommended when 500K samples are analyzed? Also it seems that we will not automatically get the tags when different models are used ("asis", "auto", "CRMA" or "CRMAv2"), so we should put the tags to differentiate them ourselves, right? Thanks! Harry --~--~---------~--~----~------------~-------~--~----~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
