Dear Christian The problem lies in the command, the bracket following the control type is not required i.e. blanks <- maText(subset=maControls(christian.raw[,1]) == "EMPTY", labels="o", col="purple") To visualise controls on a spatial plot use, maImage(christian.raw[,1], x="maControls") If this is not the problem, try typing: christian.raw into the R console and confirm that the control types are listed. If they are not, they may not have been selected whilst building the layout (use the GetInfo button in the layout widget). Regards Chris Bye > >Message: 2 >Date: Sat, 22 Nov 2003 15:44:38 +0100 >From: christian.riedel@biologie.uni-ulm.de >Subject: [BioC] (no subject) >To: bioconductor@stat.math.ethz.ch >Cc: chris_bye@wmi.usyd.edu.au >Message-ID: <1069512278.3fbf7656893f0@imap.rz.uni-ulm.de> >Content-Type: text/plain; charset=ISO-8859-1 > > >Hello, >In our Lab we are starting to run microarray analysis by using the mArray >package. We followed the 'Biologists guide to using Bioconductor' published Nov >2002 by C. Bye: >http://www.people.fas.harvard.edu/~grosu/downloads/bioconductor_manua l.pdf > >Following the instructions we modified the gal file introducing a >column "controls" to specify the blanks and N/A spots. To vizualize these >controls in MA plots we try this R code (as indicated in the guide): > >blanks<-maText(subset=maControls(christian.raw[,1]) == "EMPTY") , labels="o", >col="purple") >maPlot(christian.raw[,1], text.func = blanks) > >We tried to exchange "EMPTY" by any control specified and even tried "Control" >In any case this resulted in a "syntax error" > >We crosschecked whether these controls are accesible with the following code: > >maImage(christian.raw[,1], x="maControls) > >There we get a warning message and no plot. > >Here is an extract of our modified gal file. To our knowledge this should be ok. > >Block Row Column ID Name Controls >4 21 5 H200021155 Homo sapiens cDNA FLJ30327 fis OK >4 21 7 H200021179 Homo sapiens cDNA FLJ32985 fi OK >4 21 8 H200021185 Homo sapiens cDNA FLJ30893 fis OK >4 21 9 n/a n/a NA >4 21 16 n/a n/a NA >4 22 3 Blank Blank EMPTY >4 22 5 Blank Blank EMPTY > >Does anybody know how to handle this operation (visualization of control spots >specified in the gal file) or if we made some other mistake? > >Thanks (in advance) for help, > >Christian Riedel >Ph.D. student > >