Hi, I usually use arrayQualityMetrics with less than 20-30 chips and never cared about the outputs until now. I have a 70 Affy chips study and although the graphs are useful, they are not really presentable: most of the axis legend and labels are really squashed, the typeface barely readable... I know it is probably a very newbie question but it is a new problem for me. What steps should I take to prettify the graphs? This is my usual procedure: >library(arrayQualityMetrics) >library(simpleaffy) >data<-read.affy(covdesc="covdesc") >arrayQualityMetrics(data, + outdir = getwd(), + intgroup = "Treatment", + grouprep = True, + spatial = FALSE) Thanks in advance Sylvain =================================================================== Sylvain Foisy, Ph. D. Consultant Bio-informatique / Bioinformatics Diploide.net - TI pour la vie / IT for Life Courriel: sylvain.foisy at diploide.net Web: http://www.diploide.net Tel: (514) 893-4363

Hi Sylvain, You can try calling the aqm.xxx functions separately (aqm.maplot, aqm.boxplot, aqm.heatmap and so on), as described in the vignette and set up the graphical parameters so that they suit better to your data size. Best wishes, Audrey 2010/4/28 Sylvain Foisy <sylvain.foisy@diploide.net> > Hi, > > I usually use arrayQualityMetrics with less than 20-30 chips and never > cared > about the outputs until now. I have a 70 Affy chips study and although the > graphs are useful, they are not really presentable: most of the axis legend > and labels are really squashed, the typeface barely readable... > > I know it is probably a very newbie question but it is a new problem for > me. > What steps should I take to prettify the graphs? This is my usual > procedure: > > >library(arrayQualityMetrics) > >library(simpleaffy) > >data<-read.affy(covdesc="covdesc") > >arrayQualityMetrics(data, > + outdir = getwd(), > + intgroup = "Treatment", > + grouprep = True, > + spatial = FALSE) > > Thanks in advance > > Sylvain > > > =================================================================== > > Sylvain Foisy, Ph. D. > Consultant Bio-informatique / Bioinformatics > Diploide.net - TI pour la vie / IT for Life > > Courriel: sylvain.foisy@diploide.net > Web: http://www.diploide.net > Tel: (514) 893-4363 > > _______________________________________________ > 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 > -- Audrey Kauffmann Bergonie Cancer Institute 229 Cours de l'Argonne 33076 Bordeaux France +33.5.56.33.04.53 [[alternative HTML version deleted]]