[BioC] Limma with Imagene - reading control status - NO html

Plantinga, AED a.e.d.plantinga at medgen.azg.nl
Thu Dec 4 17:05:21 MET 2003

Dear all, 
I am experiencing difficulties with setting the spot types after reading in
Imagene files: 
> targets <- readTargets() # read in Targets.txt from working dir
> targets
SlideNumber FileNameCy3 FileNameCy5 Cy3 Cy5
1 1 0_Cy3_Slide1.txt 1_Cy5_Slide1.txt Test1 Ref1
2 2 0_Cy3_Slide2.txt 1_Cy5_Slide2.txt Test2 Ref2
> files <- cbind(targets$FileNameCy3, targets$FileNameCy5) # This step is
necessary for imagene files!
> files 
[,1] [,2] 
[1,] "0_Cy3_Slide1.txt" "1_Cy5_Slide1.txt"
[2,] "0_Cy3_Slide2.txt" "1_Cy5_Slide2.txt"
> RG <- read.maimages(files, source="imagene") # read in the files
Read header information
Read 0_Cy3_Slide1.txt 
Read 1_Cy5_Slide1.txt 
Read 0_Cy3_Slide2.txt 
Read 1_Cy5_Slide2.txt 
> types <- readSpotTypes() # read from SpotTypes.txt
> types
SpotType ID Name Color
1 Gene * * black
2 Spot Control Spot brown
3 COT Control COT brown
4 Dros Control Dros* brown
5 Cy3 Control Cy3 green
6 Cy5 Control Cy5 red
> status <- controlStatus(types,RG)
Matching patterns for: 
Error in matrix(unlist(value, recursive = FALSE, use.names = FALSE), nrow =
length(rn), : 
attempt to set an attribute on NULL
As far as I know this is what the manual suggests. What am I doing wrong? Is
there a worked example that uses Imagene files? 
Kind regards, 
Edo Plantinga

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