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_manual .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

Hi Christian, You may not have read the controls information in correctly. If you type table(maControls(christian.raw)) what happen? If dat.gal is your gal file. Did you do the following: layout <- read.marrayLayout(fnames="dat.gal", ngr=12[your arraylayout], ctl.col="Controls") Cheers Jean > 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_manu al.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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >