[BioC] Problems highlight control spots in MA plots

[Jean Yee Hwa Yang]

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_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
> 
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