Thanks, this is very helpful ! Now I have another doubt. I suspect (from cgh data) that some arrays I have have 21 trisomy. Along the X explanation, I guess that would be wise not to use those array to build the reference set. So I would like to do the following:
- 6 test arrays - 20 arrays for reference Is these possible in aroma.affymetrix? I tried test <-extract(cesN,c(21:26)) reference <- extract(cesN,c(1:20)) cbs <- CbsModel(test,reference) this of course does not work, since CbsModel expects a paired analysis here Is there a workaround ? Cheers Marco On 19 Sep, 22:10, "Henrik Bengtsson" <[EMAIL PROTECTED]> wrote: > Hi. > > On Fri, Sep 19, 2008 at 4:35 AM,marco<[EMAIL PROTECTED]> wrote: > > > Dear List, > > > I wonder about how X chromosome is treated in aroma.affymetrix. > > Is the mix of male/female samples somehow taken into account, or X is > > processed as any other chromosome? > > Good idea ;) Yes, the CRMA model does take into account the fact > that different samples have different ploidies on ChrX when using the > pool of arrays as a reference. The idea is to calculate the robust > average across all arrays and correct for the bias that > non-copy-neutral samples introduce. See Section '3.2.7 Reference > signals' in: > > H. Bengtsson; R. Irizarry; B. Carvalho; T. Speed, Estimation and > assessment of raw copy numbers at the single locus level, > Bioinformatics, 2008. [pmid: 18204055] [doi: > 10.1093/bioinformatics/btn016] > > for more details. The model/method requires that at least one sample > is copy neutral, i.e. you need at least one "female" in order to > estimate a diploid reference on ChrX. The same bias-correction > method can also be used when some of samples are say trisomy 21. For > ChrY, our current model cannot give you a *diploid* ChrY reference, > but a *copy neutral* one, i.e. CN=1 (requires at least one "male"). > To the best of my understand, none of the other methods out there use > this, but instead it is common to see that only female samples are > used for the ChrX reference. See the above CRMA paper to see how much > the ChrX CN estimates are improved when you use the above > bias-corrected method instead. > > > > > In these case the female and males test array are supposed to have > > log2 values on the average over and below zero? > > I'm note sure what you mean by this, but maybe the above answered this > question too. > > So, how do you do this in aroma.affymetrix? I have on purpose avoided > giving the details on this until someone asks for it, because it > involved the use of a new kind of non-finalized sample annotation > files (SAFs). I don't want to bother people with alpha versions in > case the API/format changes. It is unlikely that it will change much > but if you can accept that it might change, I created a new vignette > explaining how to do it: > > Vignette 'Sex-chromosome bias-corrected reference signals from pooled > average'http://groups.google.com/group/aroma-affymetrix/web/sex-chromosome-bi... > > It also illustrated a lot of other things so it might be useful for others > too. > > Hope this helps > > Henrik > > > > > Regards > > >Marco --~--~---------~--~----~------------~-------~--~----~ 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 [EMAIL PROTECTED] For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
