Fwd: problem with reading gpr files
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chawla ▴ 190
@chawla-4416
Last seen 9.9 years ago
> > (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. > Here is the code: > >> library(marray) >> myfiles <- dir(pattern="gpr") >> data<-read.GenePix(myfiles) > where I get the error >> Error in `[.data.frame`(dat, , name.Rf) : undefined columns selected > > > I have also tried >> library(limma) >> myfiles <- dir(pattern="gpr") >> RG <- read.maimages(myfiles, source="genepix") > Where also I get the error >> 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'. > I have only these files, is there any way to fix the files or find the cause of error. > > Thanks > Konika Chawla > PhD Student > Department of Biology > NTNU > > > > Konika Chawla PhD Student Department of Biology NTNU [[alternative HTML version deleted]]
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boczniak767 ▴ 740
@maciej-jonczyk-3945
Last seen 5 weeks ago
Poland
> From: konika chawla <chawla at="" 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
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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]]
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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]]
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