Dear Dr Maciej I used myfiles <- dir(pattern=3D"gpr") also reads the gpr files, but just for trying it again I created a target file as prescribe on limma documentation. and then try to read the gpr files, it still gives the same error. here is the piece of code I used library(limma) targets <- readTargets("targets.txt") f <- function(x) as.numeric(x$Flags > -99) RG <- read.maimages(targets, source="genepix", wt.fun=f) and the error is : "Error in `[.data.frame`(obj, , columns[[a]]) : undefined columns selected" I guess it is something to do with the gpr files, but don't know what. Any other ideas? Thanks Konika On Mar 7, 2013, at 12:21 PM, Maciej Jończyk wrote: >> From: konika chawla <chawla@bio.ntnu.no> >> >> Subject: [BioC] Fwd: problem with reading gpr files >> (Posting it a second time ..) Hi I am new to analyzing gpr files and I am getting an error in the first stage of reading them. >> >> >> library(limma) myfiles <- dir(pattern=3D"gpr") RG <- read.maimages(myfiles, source=3D"genepix") >> >> Where also I get the error=20 >> >> Error in `[.data.frame`(obj, , columns[[a]]) : undefined columns selected >> >> I tried to look for solution but couldn't find any except that the 'gpr files should be used as obtained from genepix'. > > You're not so far from correct commands. > Please look at limma documentation - there are some clear explanations. > You have to make targets file and read it with readTargets, > then you should use read.maimages using target frame and directory with gprs. > > Hope that helps > > Best Wishes > > -- > Dr Maciej Jonczyk, > Department of Plant Molecular Ecophysiology > Faculty of Biology, University of Warsaw > 02-096 Warsaw, Miecznikowa 1 > Poland > > > > -- > This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com Konika Chawla PhD Student Department of Biology NTNU [[alternative HTML version deleted]]

Hey concerning my earlier mail I think I found the solution, it was to trick limma to read one colour data via Cy3 <- "F532 Mean" RG <- read.maimages(source="genepix",columns=list(R=Cy3,G=Cy3)) Thanks. Konika On Mar 7, 2013, at 12:21 PM, Maciej Jończyk wrote: >> From: konika chawla <chawla@bio.ntnu.no> >> >> Subject: [BioC] Fwd: problem with reading gpr files >> (Posting it a second time ..) Hi I am new to analyzing gpr files and I am getting an error in the first stage of reading them. >> >> >> library(limma) myfiles <- dir(pattern=3D"gpr") RG <- read.maimages(myfiles, source=3D"genepix") >> >> Where also I get the error=20 >> >> Error in `[.data.frame`(obj, , columns[[a]]) : undefined columns selected >> >> I tried to look for solution but couldn't find any except that the 'gpr files should be used as obtained from genepix'. > > You're not so far from correct commands. > Please look at limma documentation - there are some clear explanations. > You have to make targets file and read it with readTargets, > then you should use read.maimages using target frame and directory with gprs. > > Hope that helps > > Best Wishes > > -- > Dr Maciej Jonczyk, > Department of Plant Molecular Ecophysiology > Faculty of Biology, University of Warsaw > 02-096 Warsaw, Miecznikowa 1 > Poland > > > > -- > This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com Konika Chawla PhD Student Department of Biology NTNU [[alternative HTML version deleted]]