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("F eatureNum","Row","Col","ProbeName","ControlType","GeneName","Descripti on","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

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$Rb) write.table(DF, file = <filename>, sep = "\t", row,names = FALSE, quote = FALSE) (almost untested :-)) Cheers, - axel Axel Klenk Research Informatician Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / Switzerland Ruppert Valentino <ruppert7 at="" hotmail="" .com=""> To Sent by: BioC bioconductor-boun <bioconductor at="" stat.math.ethz.ch=""> ces at stat.math.eth cc z.ch Subject [BioC] Is there anyway I can write 02.11.2009 14:41 out data similar to reading them using read.maimages? Hello, I have big agilent files to deal with and want to know if there is a way to collapse them by reading them and writing out the maimages but with the fields I am after. The script I used to read them are as follows : targets <- readTargets("TargetsTest.txt",sep="\t") RG <- read.maimages(targets$FileName, source = "agilent", names=targets$Description, columns= list(R = "rProcessedSignal", G = "gProcessedSignal", Rb = "rBGUsed", Gb = "gBGUsed"), annotation = c("FeatureNum","Row","Col","ProbeName","ControlType","GeneName","Descr iption","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 _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com

Dear Ruppert, There is no function like "write.maimages" because there's no need for it. limma reads only the columns it needs, which means that it reads Agilent files with many columns nearly as quickly as ones with just a few columns. Besides, I don't like to alter raw data files, just on principle. It is the number 1 way to introduce difficult to trace errors. Best wishes Gordon > Date: Mon, 2 Nov 2009 13:41:38 +0000 > From: Ruppert Valentino <ruppert7 at="" hotmail.com=""> > Subject: [BioC] Is there anyway I can write out data similar to > reading them using read.maimages? > To: BioC <bioconductor at="" stat.math.ethz.ch=""> > Content-Type: text/plain; charset="iso-8859-1" > > > > 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","Des cription","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