[BioC] (no subject)

[christian.riedel at biologie.uni-ulm.de]

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