[BioC] Re: maPlot and defining controls

[Chris Bye]

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 at biologie.uni-ulm.de
>Subject: [BioC] (no subject)
>To: bioconductor at stat.math.ethz.ch
>Cc: chris_bye at wmi.usyd.edu.au
>Message-ID: <1069512278.3fbf7656893f0 at 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_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
>  
>