Thanks very much Pierre. Apologies for my confusing use of terminology. I do indeed mean that I applied ASCRMA(v2) to each batch separately.
Regards, Peter On Tuesday, January 5, 2016 at 9:22:06 PM UTC+11, Pierre Neuvial wrote: > > Dear Peter, > > First, just to make sure we are talking about the same things, when > you write "I have applied ASCRMA to each array separately.", you mean > that you applied ASCRMA(v2) to each of the two *batches* separately, > right ? In the aroma-project world, we usually reserve the word > 'array' for what you called a 'sample'. > > Then, let me recall or clarify that ASCRMA(v2) processes each or the > 28 samples separately. Therefore, it would make no difference you > applied ASCRMAv2 on a single data set of 28 samples, or to two > separate data sets, ...or to 28 separate data sets. This is why > ASCRMA(v2) is called a "single-array" method. > > From the density plots, it seems to me that the normalization was able > to make the intensity distributions more similar, which is a good sign > that part of the experimental variability has been removed. However, > I would like to emphasize that we do not expect these distributions to > be strictly identical after normalization (as would be the case if we > were performing quantile normalization). In fact, some of the > differences we see after normalization may correspond to true > biological signal. > > At first sight it seems to me that it is safe to use your normalized > data for downstream analysis. > > If you want to dig further, one thing you could do is to plot these > densities for the normal samples only. There, we do not expect much > biological variation in the densities. If there is still clear > variation between the two batches, then one possibility to reduce it > could be to force the "average" density of the normal samples of the > two batches to be identical. The transformation used for the normal > samples of each batch could then be used to normalize the other > samples of that batch. > > I hope this will help you. > > Best, > > Pierre > > > > On Tue, Jan 5, 2016 at 7:32 AM, Peter Savas <psa...@gmail.com > <javascript:>> wrote: > > Dear Group, > > > > I have 28 samples of tumour normal pairs, run on 2 GenomeWideSNP6.0 > arrays > > several months apart. Some of the pairs have members on different chips > (ie > > tumor on one, normal on the other). I am not sure about the best way to > > normalise the data such that these split pairs can be used for > downstream > > analysis. The plan is for ASCRMA, TumorBoost and then PSCBS. > > > > I have applied ASCRMA to each array separately. Probe density plots pre > and > > post this normalisation are attached. It seems that there is still some > room > > for improvement. > > > > Thank you and all the best for the new year. > > > > Regards, > > Peter > > > > -- > > -- > > 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 with website http://www.aroma-project.org/. > > To post to this group, send email to aroma-af...@googlegroups.com > <javascript:> > > To unsubscribe and other options, go to > http://www.aroma-project.org/forum/ > > > > --- > > You received this message because you are subscribed to the Google > Groups > > "aroma.affymetrix" group. > > To unsubscribe from this group and stop receiving emails from it, send > an > > email to aroma-affymetr...@googlegroups.com <javascript:>. > > For more options, visit https://groups.google.com/d/optout. > -- -- 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 with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.
