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Question: read.GenePix not opening connection
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gravatar for Amy Mikhail
12.4 years ago by
Amy Mikhail460
Amy Mikhail460 wrote:
Hi, I am new to microarray analysis and have been trying to use marray (in R 2.1.0) to read in data from GenePix (.gpr) files, but it hasn't worked... There are 6 .gpr files (e.g. samcellINF8a.gpr as below), the sample description .txt file and a .gal file in my directory (folder containing files is called Samsfish). I've been trying to copy the example in the vignette entittled "Quick Start Guide for marray". It worked fine up until the following line of code: > data <- read.GenePix(targets=SamsfishTargets) ...which gives me this error message: Error in file(con, "r") : unable to open connection In addition: Warning message: cannot open file './samcellINF8a.gpr' (or variations on a theme) Do you know what this means? What can I do about it? Many thanks, Amy ------------------------------------------- Amy Mikhail Research student University of Aberdeen Zoology Building Tillydrone Avenue Aberdeen AB24 2TZ Scotland Email: a.mikhail at abdn.ac.uk Phone: 00-44-1224-272880 (lab)
ADD COMMENTlink modified 12.4 years ago by Tony Kowal20 • written 12.4 years ago by Amy Mikhail460
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gravatar for Paquet, Agnes
12.4 years ago by
Paquet, Agnes500
Paquet, Agnes500 wrote:
Hi Amy, Did you switch your working directory to the directory containing your gpr files? By default, read.GenePix() is looking for fnames in ".". To switch directory, you can either do: datadir <- system.file("Samsfish", package = "marray") setwd(datadir) data <- read.GenePix(fnames="samcellINF11a.gpr") or data <- read.GenePix(fnames="samcellINF11a.gpr", path=datadir) I hope this will help, Agnes -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Amy Mikhail Sent: Wednesday, June 29, 2005 1:22 PM To: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] read.GenePix not opening connection Hi, Unfortunately there are more error messages; > data <- read.GenePix(fnames=SamsfishTargets$FileName) Error in file(con, "r") : unable to open connection In addition: Warning message: cannot open file './NA' and for the next one... > data <- read.GenePix(fnames="samcellINF11a.gpr") Error in file(con, "r") : unable to open connection In addition: Warning message: cannot open file './samcellINF11a.gpr' Cheers, Amy. P.s., just a thought but when I had a look in the .gpr files with notepad they specified the path for the gal file as: ATF 1.0 29 56 "Type=GenePix Results 3" "DateTime=2005/05/09 09:18:06" "Settings=" "GalFile=D:\My Documents\sam\salmonid seq database\Grasp arrays\16kGAL_txt.gal" ...which is where it is stored on the GenePix computer, not the one I'm currently working from... Could this be the problem? ---------------------------------------------------------------------- -- --- > Hmmm. I have never *just* used the targets argument. > > What happens when you try: > > data <- read.GenePix(fnames=SamsfishTargets$FileName) > > or > > data <- read.GenePix(fnames="samcellINF11a.gpr") > > ?? > > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch on behalf of Amy Mikhail > Sent: Wed 29/06/2005 8:51 PM > To: bioconductor at stat.math.ethz.ch > Cc: > Subject: Re: [BioC] read.GenePix not opening connection > > Hi, > > Code is below: > >> library(marray) >> dir(system.file("Samsfish", package = "marray")) > [1] "16kGAL.gal" "fishData.txt" "samcellINF10b.gpr" > [4] "samcellINF11a.gpr" "samcellINF12a.gpr" "samcellINF7a.gpr" > [7] "samcellINF8a.gpr" "samcellINF9a.gpr" >> datadir <- system.file("Samsfish", package = "marray") >> SamsfishTargets <- read.marrayInfo(file.path(datadir, "fishData.txt")) > data <- read.GenePix(targets=SamsfishTargets) > Error in file(con, "r") : unable to open connection > In addition: Warning message: > cannot open file './samcellINF8a.gpr' >> ?read.GenePix >> data <- read.GenePix(targets=SamsfishTargets) > Error in file(con, "r") : unable to open connection > In addition: Warning message: > cannot open file './samcellINF8a.gpr' > > The contents of fishData.txt reads: > > fileName slideNumber > 1 samcellINF7a.gpr 1 > 2 samcellINF8a.gpr 2 > 3 samcellINF9a.gpr 3 > 4 samcellINF10b.gpr 4 > 5 samcellINF11a.gpr 5 > 6 samcellINF12a.gpr 6 > > (spaces are tabs). > > So, what have I done wrong? > > Cheers, > Amy. > > ---------------------------------------------------------------------- -- --- >> Please post all your code, including the contents of whatever file you > read into SamsfishTargets. >> >> The error you are getting is because R cannot find the files you are > telling it to open. 99.999999999% of the time this is user error :-) >> >> Mick >> >> >> >> -----Original Message----- >> From: bioconductor-bounces at stat.math.ethz.ch on behalf of Amy Mikhail > Sent: Wed 29/06/2005 8:34 PM >> To: bioconductor at stat.math.ethz.ch >> Cc: >> Subject: [BioC] read.GenePix not opening connection >> >> Hi, >> >> I am new to microarray analysis and have been trying to use marray (in R > 2.1.0) to read in data from GenePix (.gpr) files, but it hasn't > worked... >> >> There are 6 .gpr files (e.g. samcellINF8a.gpr as below), the sample > description .txt file and a .gal file in my directory (folder containing > files is called Samsfish). I've been trying to copy the example in the > vignette entittled "Quick Start Guide for marray". It worked fine up > until the following line of code: >> >>> data <- read.GenePix(targets=SamsfishTargets) >> >> ...which gives me this error message: >> >> Error in file(con, "r") : unable to open connection >> In addition: Warning message: >> cannot open file './samcellINF8a.gpr' >> >> (or variations on a theme) >> >> Do you know what this means? >> >> What can I do about it? >> >> Many thanks, >> Amy >> >> >> >> ------------------------------------------- >> Amy Mikhail >> Research student >> University of Aberdeen >> Zoology Building >> Tillydrone Avenue >> Aberdeen AB24 2TZ >> Scotland >> Email: a.mikhail at abdn.ac.uk >> Phone: 00-44-1224-272880 (lab) >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 12.4 years ago by Paquet, Agnes500
Hi Agnes, Amazing! It worked! Thank you so much. Now, do I just repeat the same thing for the other 5 files? Thanks again, Amy. ---------------------------------------------------------------------- ----- > Hi Amy, > > Did you switch your working directory to the directory containing your > gpr files? By default, read.GenePix() is looking for fnames in ".". To > switch directory, you can either do: > > datadir <- system.file("Samsfish", package = "marray") > setwd(datadir) > data <- read.GenePix(fnames="samcellINF11a.gpr") > > or > > data <- read.GenePix(fnames="samcellINF11a.gpr", path=datadir) > > I hope this will help, > > Agnes > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Amy Mikhail > Sent: Wednesday, June 29, 2005 1:22 PM > To: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] read.GenePix not opening connection > > Hi, > > Unfortunately there are more error messages; > >> data <- read.GenePix(fnames=SamsfishTargets$FileName) > Error in file(con, "r") : unable to open connection > In addition: Warning message: > cannot open file './NA' > > and for the next one... > >> data <- read.GenePix(fnames="samcellINF11a.gpr") > Error in file(con, "r") : unable to open connection > In addition: Warning message: > cannot open file './samcellINF11a.gpr' > > Cheers, > Amy. > > P.s., just a thought but when I had a look in the .gpr files with > notepad > they specified the path for the gal file as: > > ATF 1.0 > 29 56 > "Type=GenePix Results 3" > "DateTime=2005/05/09 09:18:06" > "Settings=" > "GalFile=D:\My Documents\sam\salmonid seq database\Grasp > arrays\16kGAL_txt.gal" > > ...which is where it is stored on the GenePix computer, not the one I'm > currently working from... > > Could this be the problem? > > > -------------------------------------------------------------------- ---- > --- >> Hmmm. I have never *just* used the targets argument. >> >> What happens when you try: >> >> data <- read.GenePix(fnames=SamsfishTargets$FileName) >> >> or >> >> data <- read.GenePix(fnames="samcellINF11a.gpr") >> >> ?? >> >> >> >> -----Original Message----- >> From: bioconductor-bounces at stat.math.ethz.ch on behalf of Amy Mikhail >> Sent: Wed 29/06/2005 8:51 PM >> To: bioconductor at stat.math.ethz.ch >> Cc: >> Subject: Re: [BioC] read.GenePix not opening connection >> >> Hi, >> >> Code is below: >> >>> library(marray) >>> dir(system.file("Samsfish", package = "marray")) >> [1] "16kGAL.gal" "fishData.txt" "samcellINF10b.gpr" >> [4] "samcellINF11a.gpr" "samcellINF12a.gpr" "samcellINF7a.gpr" >> [7] "samcellINF8a.gpr" "samcellINF9a.gpr" >>> datadir <- system.file("Samsfish", package = "marray") >>> SamsfishTargets <- read.marrayInfo(file.path(datadir, > "fishData.txt")) >> data <- read.GenePix(targets=SamsfishTargets) >> Error in file(con, "r") : unable to open connection >> In addition: Warning message: >> cannot open file './samcellINF8a.gpr' >>> ?read.GenePix >>> data <- read.GenePix(targets=SamsfishTargets) >> Error in file(con, "r") : unable to open connection >> In addition: Warning message: >> cannot open file './samcellINF8a.gpr' >> >> The contents of fishData.txt reads: >> >> fileName slideNumber >> 1 samcellINF7a.gpr 1 >> 2 samcellINF8a.gpr 2 >> 3 samcellINF9a.gpr 3 >> 4 samcellINF10b.gpr 4 >> 5 samcellINF11a.gpr 5 >> 6 samcellINF12a.gpr 6 >> >> (spaces are tabs). >> >> So, what have I done wrong? >> >> Cheers, >> Amy. >> >> > -------------------------------------------------------------------- ---- > --- >>> Please post all your code, including the contents of whatever file > you >> read into SamsfishTargets. >>> >>> The error you are getting is because R cannot find the files you are >> telling it to open. 99.999999999% of the time this is user error :-) >>> >>> Mick >>> >>> >>> >>> -----Original Message----- >>> From: bioconductor-bounces at stat.math.ethz.ch on behalf of Amy > Mikhail >> Sent: Wed 29/06/2005 8:34 PM >>> To: bioconductor at stat.math.ethz.ch >>> Cc: >>> Subject: [BioC] read.GenePix not opening connection >>> >>> Hi, >>> >>> I am new to microarray analysis and have been trying to use marray > (in R >> 2.1.0) to read in data from GenePix (.gpr) files, but it hasn't >> worked... >>> >>> There are 6 .gpr files (e.g. samcellINF8a.gpr as below), the sample >> description .txt file and a .gal file in my directory (folder > containing >> files is called Samsfish). I've been trying to copy the example in > the >> vignette entittled "Quick Start Guide for marray". It worked fine up >> until the following line of code: >>> >>>> data <- read.GenePix(targets=SamsfishTargets) >>> >>> ...which gives me this error message: >>> >>> Error in file(con, "r") : unable to open connection >>> In addition: Warning message: >>> cannot open file './samcellINF8a.gpr' >>> >>> (or variations on a theme) >>> >>> Do you know what this means? >>> >>> What can I do about it? >>> >>> Many thanks, >>> Amy >>> >>> >>> >>> ------------------------------------------- >>> Amy Mikhail >>> Research student >>> University of Aberdeen >>> Zoology Building >>> Tillydrone Avenue >>> Aberdeen AB24 2TZ >>> Scotland >>> Email: a.mikhail at abdn.ac.uk >>> Phone: 00-44-1224-272880 (lab) >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >>> >>> >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > >
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12.4 years ago by
michael watson IAH-C3.4k wrote:
Please post all your code, including the contents of whatever file you read into SamsfishTargets. The error you are getting is because R cannot find the files you are telling it to open. 99.999999999% of the time this is user error :-) Mick -----Original Message----- From: bioconductor-bounces at stat.math.ethz.ch on behalf of Amy Mikhail Sent: Wed 29/06/2005 8:34 PM To: bioconductor at stat.math.ethz.ch Cc: Subject: [BioC] read.GenePix not opening connection Hi, I am new to microarray analysis and have been trying to use marray (in R 2.1.0) to read in data from GenePix (.gpr) files, but it hasn't worked... There are 6 .gpr files (e.g. samcellINF8a.gpr as below), the sample description .txt file and a .gal file in my directory (folder containing files is called Samsfish). I've been trying to copy the example in the vignette entittled "Quick Start Guide for marray". It worked fine up until the following line of code: > data <- read.GenePix(targets=SamsfishTargets) ...which gives me this error message: Error in file(con, "r") : unable to open connection In addition: Warning message: cannot open file './samcellINF8a.gpr' (or variations on a theme) Do you know what this means? What can I do about it? Many thanks, Amy ------------------------------------------- Amy Mikhail Research student University of Aberdeen Zoology Building Tillydrone Avenue Aberdeen AB24 2TZ Scotland Email: a.mikhail at abdn.ac.uk Phone: 00-44-1224-272880 (lab) _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 12.4 years ago by michael watson IAH-C3.4k
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gravatar for Amy Mikhail
12.4 years ago by
Amy Mikhail460
Amy Mikhail460 wrote:
Hi, Code is below: > library(marray) > dir(system.file("Samsfish", package = "marray")) [1] "16kGAL.gal" "fishData.txt" "samcellINF10b.gpr" [4] "samcellINF11a.gpr" "samcellINF12a.gpr" "samcellINF7a.gpr" [7] "samcellINF8a.gpr" "samcellINF9a.gpr" > datadir <- system.file("Samsfish", package = "marray") > SamsfishTargets <- read.marrayInfo(file.path(datadir, "fishData.txt")) data <- read.GenePix(targets=SamsfishTargets) Error in file(con, "r") : unable to open connection In addition: Warning message: cannot open file './samcellINF8a.gpr' > ?read.GenePix > data <- read.GenePix(targets=SamsfishTargets) Error in file(con, "r") : unable to open connection In addition: Warning message: cannot open file './samcellINF8a.gpr' The contents of fishData.txt reads: fileName slideNumber 1 samcellINF7a.gpr 1 2 samcellINF8a.gpr 2 3 samcellINF9a.gpr 3 4 samcellINF10b.gpr 4 5 samcellINF11a.gpr 5 6 samcellINF12a.gpr 6 (spaces are tabs). So, what have I done wrong? Cheers, Amy. ---------------------------------------------------------------------- ----- > Please post all your code, including the contents of whatever file you read into SamsfishTargets. > > The error you are getting is because R cannot find the files you are telling it to open. 99.999999999% of the time this is user error :-) > > Mick > > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch on behalf of Amy Mikhail Sent: Wed 29/06/2005 8:34 PM > To: bioconductor at stat.math.ethz.ch > Cc: > Subject: [BioC] read.GenePix not opening connection > > Hi, > > I am new to microarray analysis and have been trying to use marray (in R 2.1.0) to read in data from GenePix (.gpr) files, but it hasn't worked... > > There are 6 .gpr files (e.g. samcellINF8a.gpr as below), the sample description .txt file and a .gal file in my directory (folder containing files is called Samsfish). I've been trying to copy the example in the vignette entittled "Quick Start Guide for marray". It worked fine up until the following line of code: > >> data <- read.GenePix(targets=SamsfishTargets) > > ...which gives me this error message: > > Error in file(con, "r") : unable to open connection > In addition: Warning message: > cannot open file './samcellINF8a.gpr' > > (or variations on a theme) > > Do you know what this means? > > What can I do about it? > > Many thanks, > Amy > > > > ------------------------------------------- > Amy Mikhail > Research student > University of Aberdeen > Zoology Building > Tillydrone Avenue > Aberdeen AB24 2TZ > Scotland > Email: a.mikhail at abdn.ac.uk > Phone: 00-44-1224-272880 (lab) > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > >
ADD COMMENTlink written 12.4 years ago by Amy Mikhail460
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gravatar for michael watson IAH-C
12.4 years ago by
michael watson IAH-C3.4k wrote:
Hmmm. I have never *just* used the targets argument. What happens when you try: data <- read.GenePix(fnames=SamsfishTargets$FileName) or data <- read.GenePix(fnames="samcellINF11a.gpr") ?? -----Original Message----- From: bioconductor-bounces at stat.math.ethz.ch on behalf of Amy Mikhail Sent: Wed 29/06/2005 8:51 PM To: bioconductor at stat.math.ethz.ch Cc: Subject: Re: [BioC] read.GenePix not opening connection Hi, Code is below: > library(marray) > dir(system.file("Samsfish", package = "marray")) [1] "16kGAL.gal" "fishData.txt" "samcellINF10b.gpr" [4] "samcellINF11a.gpr" "samcellINF12a.gpr" "samcellINF7a.gpr" [7] "samcellINF8a.gpr" "samcellINF9a.gpr" > datadir <- system.file("Samsfish", package = "marray") > SamsfishTargets <- read.marrayInfo(file.path(datadir, "fishData.txt")) data <- read.GenePix(targets=SamsfishTargets) Error in file(con, "r") : unable to open connection In addition: Warning message: cannot open file './samcellINF8a.gpr' > ?read.GenePix > data <- read.GenePix(targets=SamsfishTargets) Error in file(con, "r") : unable to open connection In addition: Warning message: cannot open file './samcellINF8a.gpr' The contents of fishData.txt reads: fileName slideNumber 1 samcellINF7a.gpr 1 2 samcellINF8a.gpr 2 3 samcellINF9a.gpr 3 4 samcellINF10b.gpr 4 5 samcellINF11a.gpr 5 6 samcellINF12a.gpr 6 (spaces are tabs). So, what have I done wrong? Cheers, Amy. ---------------------------------------------------------------------- ----- > Please post all your code, including the contents of whatever file you read into SamsfishTargets. > > The error you are getting is because R cannot find the files you are telling it to open. 99.999999999% of the time this is user error :-) > > Mick > > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch on behalf of Amy Mikhail Sent: Wed 29/06/2005 8:34 PM > To: bioconductor at stat.math.ethz.ch > Cc: > Subject: [BioC] read.GenePix not opening connection > > Hi, > > I am new to microarray analysis and have been trying to use marray (in R 2.1.0) to read in data from GenePix (.gpr) files, but it hasn't worked... > > There are 6 .gpr files (e.g. samcellINF8a.gpr as below), the sample description .txt file and a .gal file in my directory (folder containing files is called Samsfish). I've been trying to copy the example in the vignette entittled "Quick Start Guide for marray". It worked fine up until the following line of code: > >> data <- read.GenePix(targets=SamsfishTargets) > > ...which gives me this error message: > > Error in file(con, "r") : unable to open connection > In addition: Warning message: > cannot open file './samcellINF8a.gpr' > > (or variations on a theme) > > Do you know what this means? > > What can I do about it? > > Many thanks, > Amy > > > > ------------------------------------------- > Amy Mikhail > Research student > University of Aberdeen > Zoology Building > Tillydrone Avenue > Aberdeen AB24 2TZ > Scotland > Email: a.mikhail at abdn.ac.uk > Phone: 00-44-1224-272880 (lab) > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 12.4 years ago by michael watson IAH-C3.4k
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gravatar for Amy Mikhail
12.4 years ago by
Amy Mikhail460
Amy Mikhail460 wrote:
Hi, Unfortunately there are more error messages; > data <- read.GenePix(fnames=SamsfishTargets$FileName) Error in file(con, "r") : unable to open connection In addition: Warning message: cannot open file './NA' and for the next one... > data <- read.GenePix(fnames="samcellINF11a.gpr") Error in file(con, "r") : unable to open connection In addition: Warning message: cannot open file './samcellINF11a.gpr' Cheers, Amy. P.s., just a thought but when I had a look in the .gpr files with notepad they specified the path for the gal file as: ATF 1.0 29 56 "Type=GenePix Results 3" "DateTime=2005/05/09 09:18:06" "Settings=" "GalFile=D:\My Documents\sam\salmonid seq database\Grasp arrays\16kGAL_txt.gal" ...which is where it is stored on the GenePix computer, not the one I'm currently working from... Could this be the problem? ---------------------------------------------------------------------- ----- > Hmmm. I have never *just* used the targets argument. > > What happens when you try: > > data <- read.GenePix(fnames=SamsfishTargets$FileName) > > or > > data <- read.GenePix(fnames="samcellINF11a.gpr") > > ?? > > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch on behalf of Amy Mikhail > Sent: Wed 29/06/2005 8:51 PM > To: bioconductor at stat.math.ethz.ch > Cc: > Subject: Re: [BioC] read.GenePix not opening connection > > Hi, > > Code is below: > >> library(marray) >> dir(system.file("Samsfish", package = "marray")) > [1] "16kGAL.gal" "fishData.txt" "samcellINF10b.gpr" > [4] "samcellINF11a.gpr" "samcellINF12a.gpr" "samcellINF7a.gpr" > [7] "samcellINF8a.gpr" "samcellINF9a.gpr" >> datadir <- system.file("Samsfish", package = "marray") >> SamsfishTargets <- read.marrayInfo(file.path(datadir, "fishData.txt")) > data <- read.GenePix(targets=SamsfishTargets) > Error in file(con, "r") : unable to open connection > In addition: Warning message: > cannot open file './samcellINF8a.gpr' >> ?read.GenePix >> data <- read.GenePix(targets=SamsfishTargets) > Error in file(con, "r") : unable to open connection > In addition: Warning message: > cannot open file './samcellINF8a.gpr' > > The contents of fishData.txt reads: > > fileName slideNumber > 1 samcellINF7a.gpr 1 > 2 samcellINF8a.gpr 2 > 3 samcellINF9a.gpr 3 > 4 samcellINF10b.gpr 4 > 5 samcellINF11a.gpr 5 > 6 samcellINF12a.gpr 6 > > (spaces are tabs). > > So, what have I done wrong? > > Cheers, > Amy. > > -------------------------------------------------------------------- ------- >> Please post all your code, including the contents of whatever file you > read into SamsfishTargets. >> >> The error you are getting is because R cannot find the files you are > telling it to open. 99.999999999% of the time this is user error :-) >> >> Mick >> >> >> >> -----Original Message----- >> From: bioconductor-bounces at stat.math.ethz.ch on behalf of Amy Mikhail > Sent: Wed 29/06/2005 8:34 PM >> To: bioconductor at stat.math.ethz.ch >> Cc: >> Subject: [BioC] read.GenePix not opening connection >> >> Hi, >> >> I am new to microarray analysis and have been trying to use marray (in R > 2.1.0) to read in data from GenePix (.gpr) files, but it hasn't > worked... >> >> There are 6 .gpr files (e.g. samcellINF8a.gpr as below), the sample > description .txt file and a .gal file in my directory (folder containing > files is called Samsfish). I've been trying to copy the example in the > vignette entittled "Quick Start Guide for marray". It worked fine up > until the following line of code: >> >>> data <- read.GenePix(targets=SamsfishTargets) >> >> ...which gives me this error message: >> >> Error in file(con, "r") : unable to open connection >> In addition: Warning message: >> cannot open file './samcellINF8a.gpr' >> >> (or variations on a theme) >> >> Do you know what this means? >> >> What can I do about it? >> >> Many thanks, >> Amy >> >> >> >> ------------------------------------------- >> Amy Mikhail >> Research student >> University of Aberdeen >> Zoology Building >> Tillydrone Avenue >> Aberdeen AB24 2TZ >> Scotland >> Email: a.mikhail at abdn.ac.uk >> Phone: 00-44-1224-272880 (lab) >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > >
ADD COMMENTlink written 12.4 years ago by Amy Mikhail460
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gravatar for michael watson IAH-C
12.4 years ago by
michael watson IAH-C3.4k wrote:
OK, try: data <- read.GenePix(fnames="samcellINF11a.gpr", path="C:\\full\\path\\to\\my\\files\\") Mick -----Original Message----- From: bioconductor-bounces at stat.math.ethz.ch on behalf of Amy Mikhail Sent: Wed 29/06/2005 9:21 PM To: bioconductor at stat.math.ethz.ch Cc: Subject: Re: [BioC] read.GenePix not opening connection Hi, Unfortunately there are more error messages; > data <- read.GenePix(fnames=SamsfishTargets$FileName) Error in file(con, "r") : unable to open connection In addition: Warning message: cannot open file './NA' and for the next one... > data <- read.GenePix(fnames="samcellINF11a.gpr") Error in file(con, "r") : unable to open connection In addition: Warning message: cannot open file './samcellINF11a.gpr' Cheers, Amy. P.s., just a thought but when I had a look in the .gpr files with notepad they specified the path for the gal file as: ATF 1.0 29 56 "Type=GenePix Results 3" "DateTime=2005/05/09 09:18:06" "Settings=" "GalFile=D:\My Documents\sam\salmonid seq database\Grasp arrays\16kGAL_txt.gal" ...which is where it is stored on the GenePix computer, not the one I'm currently working from... Could this be the problem? ---------------------------------------------------------------------- ----- > Hmmm. I have never *just* used the targets argument. > > What happens when you try: > > data <- read.GenePix(fnames=SamsfishTargets$FileName) > > or > > data <- read.GenePix(fnames="samcellINF11a.gpr") > > ?? > > > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch on behalf of Amy Mikhail > Sent: Wed 29/06/2005 8:51 PM > To: bioconductor at stat.math.ethz.ch > Cc: > Subject: Re: [BioC] read.GenePix not opening connection > > Hi, > > Code is below: > >> library(marray) >> dir(system.file("Samsfish", package = "marray")) > [1] "16kGAL.gal" "fishData.txt" "samcellINF10b.gpr" > [4] "samcellINF11a.gpr" "samcellINF12a.gpr" "samcellINF7a.gpr" > [7] "samcellINF8a.gpr" "samcellINF9a.gpr" >> datadir <- system.file("Samsfish", package = "marray") >> SamsfishTargets <- read.marrayInfo(file.path(datadir, "fishData.txt")) > data <- read.GenePix(targets=SamsfishTargets) > Error in file(con, "r") : unable to open connection > In addition: Warning message: > cannot open file './samcellINF8a.gpr' >> ?read.GenePix >> data <- read.GenePix(targets=SamsfishTargets) > Error in file(con, "r") : unable to open connection > In addition: Warning message: > cannot open file './samcellINF8a.gpr' > > The contents of fishData.txt reads: > > fileName slideNumber > 1 samcellINF7a.gpr 1 > 2 samcellINF8a.gpr 2 > 3 samcellINF9a.gpr 3 > 4 samcellINF10b.gpr 4 > 5 samcellINF11a.gpr 5 > 6 samcellINF12a.gpr 6 > > (spaces are tabs). > > So, what have I done wrong? > > Cheers, > Amy. > > -------------------------------------------------------------------- ------- >> Please post all your code, including the contents of whatever file you > read into SamsfishTargets. >> >> The error you are getting is because R cannot find the files you are > telling it to open. 99.999999999% of the time this is user error :-) >> >> Mick >> >> >> >> -----Original Message----- >> From: bioconductor-bounces at stat.math.ethz.ch on behalf of Amy Mikhail > Sent: Wed 29/06/2005 8:34 PM >> To: bioconductor at stat.math.ethz.ch >> Cc: >> Subject: [BioC] read.GenePix not opening connection >> >> Hi, >> >> I am new to microarray analysis and have been trying to use marray (in R > 2.1.0) to read in data from GenePix (.gpr) files, but it hasn't > worked... >> >> There are 6 .gpr files (e.g. samcellINF8a.gpr as below), the sample > description .txt file and a .gal file in my directory (folder containing > files is called Samsfish). I've been trying to copy the example in the > vignette entittled "Quick Start Guide for marray". It worked fine up > until the following line of code: >> >>> data <- read.GenePix(targets=SamsfishTargets) >> >> ...which gives me this error message: >> >> Error in file(con, "r") : unable to open connection >> In addition: Warning message: >> cannot open file './samcellINF8a.gpr' >> >> (or variations on a theme) >> >> Do you know what this means? >> >> What can I do about it? >> >> Many thanks, >> Amy >> >> >> >> ------------------------------------------- >> Amy Mikhail >> Research student >> University of Aberdeen >> Zoology Building >> Tillydrone Avenue >> Aberdeen AB24 2TZ >> Scotland >> Email: a.mikhail at abdn.ac.uk >> Phone: 00-44-1224-272880 (lab) >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 12.4 years ago by michael watson IAH-C3.4k
0
gravatar for Amy Mikhail
12.4 years ago by
Amy Mikhail460
Amy Mikhail460 wrote:
Hi, Yet another error message... > data <- read.GenePix(fnames="samcellINF11a.gpr", + path="C:\\full\\path\\to\\my\\files\\") Error in file(con, "r") : unable to open connection In addition: Warning message: cannot open file 'C:\full\path\to\my\files\/samcellINF11a.gpr' Any ideas? Cheers, Amy. ---------------------------------------------------------------------- ----- > OK, try: > > data <- read.GenePix(fnames="samcellINF11a.gpr", > path="C:\\full\\path\\to\\my\\files\\") > > Mick > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch on behalf of Amy Mikhail > Sent: Wed 29/06/2005 9:21 PM > To: bioconductor at stat.math.ethz.ch > Cc: > Subject: Re: [BioC] read.GenePix not opening connection > > Hi, > > Unfortunately there are more error messages; > >> data <- read.GenePix(fnames=SamsfishTargets$FileName) > Error in file(con, "r") : unable to open connection > In addition: Warning message: > cannot open file './NA' > > and for the next one... > >> data <- read.GenePix(fnames="samcellINF11a.gpr") > Error in file(con, "r") : unable to open connection > In addition: Warning message: > cannot open file './samcellINF11a.gpr' > > Cheers, > Amy. > > P.s., just a thought but when I had a look in the .gpr files with notepad > they specified the path for the gal file as: > > ATF 1.0 > 29 56 > "Type=GenePix Results 3" > "DateTime=2005/05/09 09:18:06" > "Settings=" > "GalFile=D:\My Documents\sam\salmonid seq database\Grasp > arrays\16kGAL_txt.gal" > > ...which is where it is stored on the GenePix computer, not the one I'm > currently working from... > > Could this be the problem? > > > -------------------------------------------------------------------- ------- >> Hmmm. I have never *just* used the targets argument. >> >> What happens when you try: >> >> data <- read.GenePix(fnames=SamsfishTargets$FileName) >> >> or >> >> data <- read.GenePix(fnames="samcellINF11a.gpr") >> >> ?? >> >> >> >> -----Original Message----- >> From: bioconductor-bounces at stat.math.ethz.ch on behalf of Amy Mikhail >> Sent: Wed 29/06/2005 8:51 PM >> To: bioconductor at stat.math.ethz.ch >> Cc: >> Subject: Re: [BioC] read.GenePix not opening connection >> >> Hi, >> >> Code is below: >> >>> library(marray) >>> dir(system.file("Samsfish", package = "marray")) >> [1] "16kGAL.gal" "fishData.txt" "samcellINF10b.gpr" >> [4] "samcellINF11a.gpr" "samcellINF12a.gpr" "samcellINF7a.gpr" >> [7] "samcellINF8a.gpr" "samcellINF9a.gpr" >>> datadir <- system.file("Samsfish", package = "marray") >>> SamsfishTargets <- read.marrayInfo(file.path(datadir, "fishData.txt")) >> data <- read.GenePix(targets=SamsfishTargets) >> Error in file(con, "r") : unable to open connection >> In addition: Warning message: >> cannot open file './samcellINF8a.gpr' >>> ?read.GenePix >>> data <- read.GenePix(targets=SamsfishTargets) >> Error in file(con, "r") : unable to open connection >> In addition: Warning message: >> cannot open file './samcellINF8a.gpr' >> >> The contents of fishData.txt reads: >> >> fileName slideNumber >> 1 samcellINF7a.gpr 1 >> 2 samcellINF8a.gpr 2 >> 3 samcellINF9a.gpr 3 >> 4 samcellINF10b.gpr 4 >> 5 samcellINF11a.gpr 5 >> 6 samcellINF12a.gpr 6 >> >> (spaces are tabs). >> >> So, what have I done wrong? >> >> Cheers, >> Amy. >> >> ------------------------------------------------------------------- -------- >>> Please post all your code, including the contents of whatever file you >> read into SamsfishTargets. >>> >>> The error you are getting is because R cannot find the files you are >> telling it to open. 99.999999999% of the time this is user error :-) >>> >>> Mick >>> >>> >>> >>> -----Original Message----- >>> From: bioconductor-bounces at stat.math.ethz.ch on behalf of Amy Mikhail >> Sent: Wed 29/06/2005 8:34 PM >>> To: bioconductor at stat.math.ethz.ch >>> Cc: >>> Subject: [BioC] read.GenePix not opening connection >>> >>> Hi, >>> >>> I am new to microarray analysis and have been trying to use marray (in >>> R >> 2.1.0) to read in data from GenePix (.gpr) files, but it hasn't >> worked... >>> >>> There are 6 .gpr files (e.g. samcellINF8a.gpr as below), the sample >> description .txt file and a .gal file in my directory (folder containing >> files is called Samsfish). I've been trying to copy the example in the >> vignette entittled "Quick Start Guide for marray". It worked fine up >> until the following line of code: >>> >>>> data <- read.GenePix(targets=SamsfishTargets) >>> >>> ...which gives me this error message: >>> >>> Error in file(con, "r") : unable to open connection >>> In addition: Warning message: >>> cannot open file './samcellINF8a.gpr' >>> >>> (or variations on a theme) >>> >>> Do you know what this means? >>> >>> What can I do about it? >>> >>> Many thanks, >>> Amy >>> >>> >>> >>> ------------------------------------------- >>> Amy Mikhail >>> Research student >>> University of Aberdeen >>> Zoology Building >>> Tillydrone Avenue >>> Aberdeen AB24 2TZ >>> Scotland >>> Email: a.mikhail at abdn.ac.uk >>> Phone: 00-44-1224-272880 (lab) >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >>> >>> >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> >> >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > >
ADD COMMENTlink written 12.4 years ago by Amy Mikhail460
0
gravatar for Amy Mikhail
12.4 years ago by
Amy Mikhail460
Amy Mikhail460 wrote:
Hi, Forgive my ignorance but what is R(D) Com software? Is that a package? Cheers, Amy. ---------------------------------------------------------------------- ----- > Hi - > > I was wondering if the problem could be that the R(D)Com software was not > installed when > you installed R?? Does anyone know if that could be the problem? > > Tony > > > > ==============Original message text=============== > On Wed, 29 Jun 2005 3:46:55 pm CDT "Amy Mikhail" wrote: > > Hi, > > Yet another error message... > >> data <- read.GenePix(fnames="samcellINF11a.gpr", > + path="C:\\full\\path\\to\\my\\files\\") > Error in file(con, "r") : unable to open connection > In addition: Warning message: > cannot open file 'C:\full\path\to\my\files\/samcellINF11a.gpr' > > Any ideas? > > Cheers, > Amy. > -------------------------------------------------------------------- ------- > > > > Tony Kowal > Graduate Student > Rex Chisholm Laboratory > > Northwestern University > 303 E. Superior > Lurie Building > Room 7-250 > Chicago, IL 60611 > > Lab: 312 503 4169 > e-mail: askowal at northwestern.edu > > > >
ADD COMMENTlink written 12.4 years ago by Amy Mikhail460
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