[BioC] Is there anyway I can write out data similar to reading them using read.maimages?

[axel.klenk at actelion.com]

Dear Ruppert,

I think RGList objects are intended for further analysis, not for
exporting...

Do you want to collapse the individual files? I'd use a combination of
read.delim() and write.table() in a loop; see ?read.delim and its
colClasses
argument for specifying which columns to read.

Alternatively, for exporting the dataset as a whole, I'd try something like

DF <- cbind(RG$genes, G = RG$G, Gb = RG$Gb, R = RG$R, Rb = RG$Rb)
write.table(DF, file = <FILENAME>, sep = "\t", row,names = FALSE, quote =
FALSE)
(almost untested :-))

Cheers,

 - axel


Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil /
Switzerland



                                                                           
             Ruppert Valentino                                             
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                                                                   Subject 
                                       [BioC] Is there anyway I can write  
             02.11.2009 14:41          out data similar to reading them    
                                       using read.maimages?                
                                                                           
                                                                           
                                                                           
                                                                           
                                                                           
                                                                           






Hello,

I have big agilent files to deal with and want to know if there is a way to
collapse them by reading them and writing out the maimages but with the
fields I am after.

The script I used to read them are as follows :


targets <- readTargets("TargetsTest.txt",sep="\t")

RG <- read.maimages(targets$FileName, source = "agilent",
names=targets$Description, columns= list(R = "rProcessedSignal", G =
"gProcessedSignal", Rb = "rBGUsed", Gb = "gBGUsed"), annotation =
c("FeatureNum","Row","Col","ProbeName","ControlType","GeneName","Description","SystematicName"))



there is no function called write.maimages but is there something similar
that would take the RG attributes and write them out so they can be read
later using read.maimages?


thanks




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