Hi Alexandre, The tools NetAffx and liftOver use different methods to map data. Which is "better" is a decision that you will have to make.
To learn more about the liftOver program, you could read the Methods for the Chain and Net tracks in the UCSC Browser, since the liftOver tool uses derivative data based on those alignments. Unfortunately, you will need to contact Affymetrix to get support for their tool set. If you find differences that you think are errors, they would also be the best contact to report these too. Thanks! Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/2/10 7:50 AM, alexandre beck wrote: > Hello everyone. > > I'm looking for compare affymetrix probe set expression from > the different probe cell positions on gene. I downloaded the affymetrix > annotation file about HG U133 plus 2 microarray (HG 18 and HG 17) and I > converted them into HG 19 model with Lift Over tool. > The problem is the folowing: when I compare result with data provided by > affymetrix (NetAffx tool), I obtain some times the same data (i.e. probe set > 1007_s_at) and sometimes conflicting data (i.e. probe set 1053_at). > Furthermore, Genome browser seems to generaly agree whith affymetrix data. > I would like to understand why I founded these diferencies and which are the > best data to use. > I may did something wrong and someone may correct me in my protocol > Thanks for your attention > Best regards > Alexandre > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
