Tim, Thanks for your answer!! Hajar 2010/11/12 Tim Triche <tim.triche@gmail.com> > yes -- the text files have local bgcorrection applied. > > truncate the intensities at a minimum of 0 or 1 if the > negative-photons-bouncing-off-the-array business bothers you (what with it > being at odds with the way the universe works and all). This also avoids > later irritations from other libraries. > > > > On Fri, Nov 12, 2010 at 1:35 PM, Hajar Hassani Lahsinoui < > hajar.hassani@gmail.com> wrote: > >> Hi everyone, >> >> I tried to read beadarry data in R with backgroundMethod="none". For some >> reason it still gives me the array's with a background correction. See >> below. Does this mean my "raw data" has allready been background corrected? >> I couldn't find it in the report. >> >> Thanks, >> >> Hajar >> >> >> BLData=readIllumina(arrayNames=array.namen,backgroundMethod="none", normalizeMethod="Quantile",useImages=F) >> 'useImages=FALSE': please check that the 'singleChannel' >> argument is appropriate for your data set >> Found 24 arrays >> Reading raw data from ./5513091009_A_perBeadFile.txt >> Reading locally background corrected intensities >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > -- > If people do not believe that mathematics is simple, it is only because > they do not realize how complicated life is. > John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html=""> > > [[alternative HTML version deleted]]