[2nd repost of this message - now from the Google Group web interface; still problems with the Google forum.]
Hi Nicolas. On Tue, Jul 20, 2010 at 11:42 AM, Nicolas Vergne <nicolas.vergne....@gmail.com> wrote: > Hi everybody, > > I use ACNE for the normalization of SNP6.0 chip arrays. > As ACNE is a multi-array methode, I would like to know if there is an > option to precise the dataset of reference in the doACNE function? - Show quoted text - > I would like to use the same sample for each new chip normalization. And > I wouldn't like to use the dataset that I want to normalize. Is it a > good way? My problem is to not reproduce the analysis for each new > chip in the project. This sounds like the (b) alternative: It is rather well known that there are large lab and batch effects in Affymetrix data. Preprocessing removes some of this but certainly not everything. Others have observed this over and over. Because of this, estimating the ACNE model parameters on one data set from a different batch/lab and use them to normalize another data set will work less well than if the parameters where estimated from samples with the same batch. Hope this helps (a bit). /Henrik > > Thanks in advance for your answers, > > Nicolas -- 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/
