Thanks for your email Henrik. > When you say heterogeneous, do you mean that they contain a lot of CN > aberrations or do you mean that they have different noise levels?
Different noise levels. > > If "not too many" things go on in your reference samples, then you > should expect to get an improvement when you calculate the reference > channel as the average over a larger and larger pool of samples. A > few years ago I checked this on 500K data and I found a dramatic drop > in SNRs when increasing from 5 to 10 to 20 reference samples and then > i flattened out. > > However, if you look Nannya et al (2005), their CNAG method tries to > identify a subset of reference samples that gives best SNRs. This is > to say that you believe there is a set of reference samples that are > more "normal" than others. An alternative argument, which may make > even more sense is that there will always be some systematic effects > remaining in the estimates and if you can locate a set of reference > samples that have similar remaining effects as you test sample, they > will cancel out better than if other reference samples where used. > Note that this strategy uses different pools of references for each > test sample. I know that the Broad Institute (Gaddy Getz, Scott > Carter et al.) are doing something similar in the TCGA project and > they say they get better SNRs. thank you very much for these pointers, I'll look into them. I'll try and do something a bit more systematic and post the results. cheers Lavinia. --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
