Dear users, I have created a directory with a white-space delimited file describing my samples called "covdesc" as suggested and have all the CEL files in the same directory I have loaded simpleaffy library and tried to read in the data. I get an error that has been previously mentioned but couldn?t find the solution in the Bioconductor Archives. This is what I type and the error > raw.data <- read.affy() Error in file(file, "r") : unable to open connection In addition: Warning message: cannot open file `./covdesc' I am working on a Windows 2000 computer R version 1.9.1 BioC version 1.4 any suggestions? Thanks in advance David

That error usually indicates that you have not set the working directory to the directory containing your files. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> <kfbargad@lg.ehu.es> 07/01/04 12:58PM >>> Dear users, I have created a directory with a white-space delimited file describing my samples called "covdesc" as suggested and have all the CEL files in the same directory I have loaded simpleaffy library and tried to read in the data. I get an error that has been previously mentioned but couldn t find the solution in the Bioconductor Archives. This is what I type and the error > raw.data <- read.affy() Error in file(file, "r") : unable to open connection In addition: Warning message: cannot open file `./covdesc' I am working on a Windows 2000 computer R version 1.9.1 BioC version 1.4 any suggestions? Thanks in advance David _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Thanks Jim for your quick answer. My working directory is the right one because if I use the affy package I can read in the data: > library(simpleaffy) > library(affy) > raw.data <- read.affy() Error in file(file, "r") : unable to open connection In addition: Warning message: cannot open file `./covdesc' > Data <- ReadAffy() > Data AffyBatch object size of arrays=712x712 features (23767 kb) cdf=HG-U133A (22283 affyids) number of samples=6 number of genes=22283 annotation=hgu133a > That error usually indicates that you have not set the working directory > to the directory containing your files. > > HTH, > > Jim > > > > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > >>> <kfbargad@lg.ehu.es> 07/01/04 12:58PM >>> > > Dear users, > > I have created a directory with a white-space delimited file > describing my samples called "covdesc" as suggested and have all the > CEL files in the same directory > > I have loaded simpleaffy library and tried to read in the data. I get > > an error that has been previously mentioned but couldn t find the > solution in the Bioconductor Archives. This is what I type and the > error > > > raw.data <- read.affy() > Error in file(file, "r") : unable to open connection > In addition: Warning message: > cannot open file `./covdesc' > > I am working on a Windows 2000 computer > R version 1.9.1 > BioC version 1.4 > > any suggestions? > > > Thanks in advance > > David > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

Hi, Do you have a file in the directory called 'covdesc'... It should contain the information about your experimental factors for your arrays: For example: A B One.cel n n Two.cel n y Three.cell y y Four.cel n n Five.cel n y Six.cel y y Seven.cel n n Eight.cel n y Nine.cel y y These end up in the pData slot of the AffyBatch object that gets read in... (you can specify the name of the file you are looking for: eset <- covdesc("my.design.file") or whatever)... Crispin -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of kfbargad@lg.ehu.es Sent: 02 July 2004 07:50 To: Bioconductor@stat.math.ethz.ch Subject: Re: [BioC] simpleaffy error Thanks Jim for your quick answer. My working directory is the right one because if I use the affy package I can read in the data: > library(simpleaffy) > library(affy) > raw.data <- read.affy() Error in file(file, "r") : unable to open connection In addition: Warning message: cannot open file `./covdesc' > Data <- ReadAffy() > Data AffyBatch object size of arrays=712x712 features (23767 kb) cdf=HG-U133A (22283 affyids) number of samples=6 number of genes=22283 annotation=hgu133a > That error usually indicates that you have not set the working directory > to the directory containing your files. > > HTH, > > Jim > > > > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > >>> <kfbargad@lg.ehu.es> 07/01/04 12:58PM >>> > > Dear users, > > I have created a directory with a white-space delimited file > describing my samples called "covdesc" as suggested and have all the > CEL files in the same directory > > I have loaded simpleaffy library and tried to read in the data. I get > > an error that has been previously mentioned but couldn t find the > solution in the Bioconductor Archives. This is what I type and the > error > > > raw.data <- read.affy() > Error in file(file, "r") : unable to open connection In addition: > Warning message: > cannot open file `./covdesc' > > I am working on a Windows 2000 computer R version 1.9.1 BioC version > 1.4 > > any suggestions? > > > Thanks in advance > > David > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}

Ok, Sorry about my earlier suggestion - I've now read the email properly... ;-) I suspect that it's a problem with using '/' as a path separator on Windows... (I see you're using a Windows system...) I'll have a play and get back to you.. Crispin p.s. note that I've not tested things recently on windows: http://bioinformatics.picr.man.ac.uk/simpleaffy -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of kfbargad@lg.ehu.es Sent: 02 July 2004 07:50 To: Bioconductor@stat.math.ethz.ch Subject: Re: [BioC] simpleaffy error Thanks Jim for your quick answer. My working directory is the right one because if I use the affy package I can read in the data: > library(simpleaffy) > library(affy) > raw.data <- read.affy() Error in file(file, "r") : unable to open connection In addition: Warning message: cannot open file `./covdesc' > Data <- ReadAffy() > Data AffyBatch object size of arrays=712x712 features (23767 kb) cdf=HG-U133A (22283 affyids) number of samples=6 number of genes=22283 annotation=hgu133a * SNIP * -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}

Crispin, I don't think it has to do with using '/' as a path separator on Windows, because this works for me. David, Is your covdesc by chance called covdesc.txt? If I have a file named covdesc in my working directory, it works fine. If the file is missing or has a .txt subscript, then I get the error you report. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Crispin Miller" <cmiller@picr.man.ac.uk> 07/02/04 07:50AM >>> Ok, Sorry about my earlier suggestion - I've now read the email properly... ;-) I suspect that it's a problem with using '/' as a path separator on Windows... (I see you're using a Windows system...) I'll have a play and get back to you.. Crispin p.s. note that I've not tested things recently on windows: http://bioinformatics.picr.man.ac.uk/simpleaffy -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of kfbargad@lg.ehu.es Sent: 02 July 2004 07:50 To: Bioconductor@stat.math.ethz.ch Subject: Re: [BioC] simpleaffy error Thanks Jim for your quick answer. My working directory is the right one because if I use the affy package I can read in the data: > library(simpleaffy) > library(affy) > raw.data <- read.affy() Error in file(file, "r") : unable to open connection In addition: Warning message: cannot open file `./covdesc' > Data <- ReadAffy() > Data AffyBatch object size of arrays=712x712 features (23767 kb) cdf=HG-U133A (22283 affyids) number of samples=6 number of genes=22283 annotation=hgu133a * SNIP * -------------------------------------------------------- This email is confidential and intended solely for the use\ ...{{dropped}}

Dear James, I have tried typing the following: > raw.data<-read.affy("covdesc.txt") Error in read.affybatch(filenames = filenames, phenoData = phenoData, : Could not open file ./DEP014HA But I can still read in my Cel files with affy: > raw.data <- ReadAffy() > raw.data AffyBatch object size of arrays=712x712 features (23767 kb) cdf=HG-U133A (22283 affyids) number of samples=6 number of genes=22283 annotation=hgu133a David > Crispin, > > I don't think it has to do with using '/' as a path separator on > Windows, because this works for me. > > David, > > Is your covdesc by chance called covdesc.txt? If I have a file named > covdesc in my working directory, it works fine. If the file is missing > or has a .txt subscript, then I get the error you report. > > HTH, > > Jim > > > > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > >>> "Crispin Miller" <cmiller@picr.man.ac.uk> 07/02/04 07:50AM >>> > Ok, > > Sorry about my earlier suggestion - I've now read the email > properly... > ;-) > I suspect that it's a problem with using '/' as a path separator on > Windows... (I see you're using a Windows system...) I'll have a play > and > get back to you.. > Crispin > p.s. note that I've not tested things recently on windows: > http://bioinformatics.picr.man.ac.uk/simpleaffy > > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of > kfbargad@lg.ehu.es > Sent: 02 July 2004 07:50 > To: Bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] simpleaffy error > > Thanks Jim for your quick answer. My working directory is the right > one > because if I use the affy package I can read in the data: > > > library(simpleaffy) > > library(affy) > > raw.data <- read.affy() > Error in file(file, "r") : unable to open connection In addition: > Warning message: > cannot open file `./covdesc' > > Data <- ReadAffy() > > Data > AffyBatch object > size of arrays=712x712 features (23767 kb) cdf=HG-U133A (22283 > affyids) > number of samples=6 number of genes=22283 annotation=hgu133a > > * SNIP * > > -------------------------------------------------------- > > > This email is confidential and intended solely for the use > o...{{dropped}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

Dear Crispin and James, thanks a lot for your help. I finally worked out what the problem was. Even though my covdesc file hasn?t got the file extension in its name, I still have to type in covdesc.txt. The mistake was that the names I gave the samples in the covdesc file were slightly different than the CEL files, since the names of the CEL files have a date and I didn?t add that to the covdesc file. How can I make sure that the parameters have been associated to the samples? Thanks David