[BioC] Limma with Imagene - reading control status - NO
smyth at wehi.edu.au
Sat Dec 6 01:41:20 MET 2003
The problem is that your gene list doesn't have columns called "ID" and
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)
to get a color-coded MA-plot. I have used a similar example successfully
myself with Imagene data.
At 03:05 AM 5/12/2003, Plantinga, AED wrote:
>I am experiencing difficulties with setting the spot types after reading in
> > 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,] "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
> > 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 =
>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?
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