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 [[alternative HTML version deleted]]

The problem is that your gene list doesn't have columns called "ID" and "Name". Type names(RG$genes) With Imagene data you will probably find a column called "Gene ID". The regular expression columns in your SpotTypes file must match columns in your gene list. I have made some updates to limma which should solve your problems. You will need to update to limma 1.3.6 available now from http://bioinf.wehi.edu.au/limma or very soon from the Bioconductor development packages area. Assuming that your gene list does have a column "Gene ID" (you need to check this), you will want a SpotTypes file something like: SpotType Gene ID col cex Gene * black 0.2 Spot Spot brown 1 COT COT brown 1 Dros Dros* brown 1 Cy3 Cy3 green 1 Cy5 Cy5 red 1 You should be able to type: types <- readSpotTypes() RG$genes$Status <- controlStatus(types,RG) plotMA(RG) to get a color-coded MA-plot. I have used a similar example successfully myself with Imagene data. Gordon At 03:05 AM 5/12/2003, Plantinga, AED wrote: >Dear all, >I am experiencing difficulties with setting the spot types after reading in >Imagene files: > > targets <- readTargets() # read in Targets.txt from working dir > > targets >SlideNumber FileNameCy3 FileNameCy5 Cy3 Cy5 >1 1 0_Cy3_Slide1.txt 1_Cy5_Slide1.txt Test1 Ref1 >2 2 0_Cy3_Slide2.txt 1_Cy5_Slide2.txt Test2 Ref2 > > files <- cbind(targets$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