Dear BioC mailing list members,

I am using limma to generate MA-plots for Agilent arrays.  In these plots I would like to highlight the positive controls in red and the negative controls in blue.  To do this, in accordance with the limma User's guide, I am following these steps:

# reading the arrays in limma (from two files specified in targets.txt)
> datadir = ("...")
> targets <- readTargets("targets.txt", sep="\t", quote="\"")
> RG <- read.maimages(targets$FileName, source="agilent", path=datadir, names=targets$Sample, columns= list(R = "rMeanSignal", G ="gMeanSignal", Rb = "rBGUsed", Gb = "gBGUsed", Rb.real = "rBGMeanSignal", Gb.real = "gBGMeanSignal"), annotation = c("FeatureNum","Row","Col","ProbeName","ControlType","GeneName"))

The files are read (with an warning message)
Warning message:
In read.maimages(targets$FileName, source = "agilent", path = datadir,  :
  non-standard columns specified

Please note the presence of the fields ProbeName and ControlType in "annotation".  ControlType has three types of values: 0 for probes, -1 for negative controls and 1 for positive controls.

# reading a tab-delimited STF file (named SpotTypes.txt) of the form
SpotType    ControlType    ProbeName    Color
probe    0    *    yellow
neg    -1    *    blue
pos    1    *    red

I am setting the color to yellow for probes in order to test if the color assignment is performed in the following steps:

> setwd = (datadir)
> spottypes = readSpotTypes()
> RG$genes$ControlType = controlStatus(spottypes, RG)
Matching patterns for: ControlType ProbeName 
Found xxx probe 
Found yyy neg 
Found zzz pos 
Setting attributes: values Color 
> plotMA(RG[,1])

However, in the resulting MA-plot all points are black suggesting that the color assignment did not take place properly.  I checked the data structures and the commands and they seem to be correct.

I do not understand why this does not work and I would very much appreciate your help in solving the issue.

SessionInfo() is:
R version 2.6.1 (2007-11-26) 
i386-pc-mingw32 
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] limma_2.12.0


Thank you very much,
Dana 
       
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