[BioC] Problems highlight control spots in MA plots

christian.riedel at biologie.uni-ulm.de christian.riedel at biologie.uni-ulm.de
Sun Nov 23 18:34:24 MET 2003

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: 

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", 
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

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