[BioC] Getting additional columns from Imagene files with read.maimages from limma

[Peder Worning]

Hello Bioconductor,

I am using the read.maimages function from the limma package. But I want
to read two more columns from the Imagene files than default. I have
tried to use the other.columns variable to read the data and it works in
principle, I get the data but not in a format I can use and the "other"
option spoils my naming routine for the spots in the arrays. I'll show
some code and ask how to get around it. In this experiment I have 3
slides with 14592 spots

This is how I normally do it and each spot gets its id as the rowname
RG.NQ <- read.maimages(file.NQ, source="imagene", 
        names=target.NQ$Barcode,
        wt.fun=mywtfun(c(1,2,3,4,5,6,7)),
        columns=list(f="Signal Mean",b="Background Median"))

rownames(RG.NQ) <- RG.NQ$genes[,6]
dim(RG.NQ)
[1] 14592     3 

names(RG.NQ)
[1] "R"                "G"                "Rb"               "Gb"

[5] "source"           "Field.Dimensions" "weights"          "printer"

[9] "genes"



Here follow the new code that gives me troubles
RGp.NQ <- read.maimages(filep.NQ, source="imagene",
        names=targetp.NQ$Barcode,
        wt.fun=mywtfun(c(1,2,3,4,5,6,7)), 
        columns=list(f="Signal Mean",b="Background Median"),
        other.columns=list(t="Signal Stdev",u="Background Stdev"))
names(RGp.NQ)
 [1] "R"                "G"                "Rb"               "Gb"

 [5] "source"           "Field.Dimensions" "weights"          "other"

 [9] "printer"          "genes"
names(RGp.NQ$other)
[1] "G Signal Stdev"     "G Background Stdev" "R Signal Stdev"    
[4] "R Background Stdev" 

And here starts the problems. How do I read variable names with white
spaces \ or \\ do not work, and how do I recover the original format of
the RGp.NQ object from the list RGp.NQ$other 
dim(RGp.NQ)
[1] 14592     3
3 slides 14592 spots

Furthermore I cannot make each spot have its id as rowname

rownames(RGp.NQ) <- RGp.NQ$genes[,6]
Error in dimnames(object$other[[a]]) <- value : object "object" not
found

If anyone knows a way around these troubles I'll appreciate it a lot
because I need the Signal Stdev and the Background Stdev to evaluate the
quality of each spot.

Regards 
Peder Worning 


Best regards 

Exiqon A/S

 Peder Worning, Ph.D.

Senior Scientist, Biomarker Discovery

Telephone: +45 45650457 
Telefax: +45 45661888  
E-mail: pwo at exiqon.com

 Bygstubben 3 
DK-2950 Vedbaek 
Denmark 
www.exiqon.com