affy package problem
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@phguardiolaolcom-152
Last seen 10.3 years ago
Hi all, I m trying to use Affy 1.4.2 with U133A chips on a new PC P4 with XP Pro and R 1.8.1 I m selecting the right Folder first where my CEL files are and then paste on the command line: data1 <- ReadAffy() data2 <- gcrma(data1) exprs2excel(data2, file="Fibroalone_gcrma.csv") then I obtain the following: > library(affy) Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Synching your local package management information ... Packages which have been added/updated: matchprobes arrayMagic externalVector limma > library(gcrma) Loading required package: MASS > data1 <- ReadAffy() Error in initialize(value, ...) : Could not open file C:/Phil/CEL files Fibro alone/FANC Fibro/fibro PD331neo01.CEL > data2 <- gcrma(data1) Error: Object "data1" not found Error in probeNames(object) : Unable to find the argument "object" in selecting a method for function "probeNames" > exprs2excel(data2, file="Fibroalone_gcrma.csv and in addition, the CEL file is no more present in the folder as if it was deleted...! Any suggestion ? Thanks Philippe
affy affy • 1.5k views
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@james-w-macdonald-5106
Last seen 2 hours ago
United States
It appears that there is a bug in 1.4.2 that causes it to not read text .cel files. For now, I would recommend reverting to the release version for non-binary .cel files. 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 >>> <phguardiol@aol.com> 12/02/03 04:51AM >>> Hi all, I m trying to use Affy 1.4.2 with U133A chips on a new PC P4 with XP Pro and R 1.8.1 I m selecting the right Folder first where my CEL files are and then paste on the command line: data1 <- ReadAffy() data2 <- gcrma(data1) exprs2excel(data2, file="Fibroalone_gcrma.csv") then I obtain the following: > library(affy) Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Synching your local package management information ... Packages which have been added/updated: matchprobes arrayMagic externalVector limma > library(gcrma) Loading required package: MASS > data1 <- ReadAffy() Error in initialize(value, ...) : Could not open file C:/Phil/CEL files Fibro alone/FANC Fibro/fibro PD331neo01.CEL > data2 <- gcrma(data1) Error: Object "data1" not found Error in probeNames(object) : Unable to find the argument "object" in selecting a method for function "probeNames" > exprs2excel(data2, file="Fibroalone_gcrma.csv and in addition, the CEL file is no more present in the folder as if it was deleted...! Any suggestion ? Thanks Philippe _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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@james-w-macdonald-5106
Last seen 2 hours ago
United States
Correction: There is a bug in the Win32 version of affy 1.4.2. The *nix version appears to work fine for text .cel files. 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 >>> "James MacDonald" <jmacdon@med.umich.edu> 12/02/03 09:01AM >>> It appears that there is a bug in 1.4.2 that causes it to not read text .cel files. For now, I would recommend reverting to the release version for non-binary .cel files. 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 >>> <phguardiol@aol.com> 12/02/03 04:51AM >>> Hi all, I m trying to use Affy 1.4.2 with U133A chips on a new PC P4 with XP Pro and R 1.8.1 I m selecting the right Folder first where my CEL files are and then paste on the command line: data1 <- ReadAffy() data2 <- gcrma(data1) exprs2excel(data2, file="Fibroalone_gcrma.csv") then I obtain the following: > library(affy) Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Synching your local package management information ... Packages which have been added/updated: matchprobes arrayMagic externalVector limma > library(gcrma) Loading required package: MASS > data1 <- ReadAffy() Error in initialize(value, ...) : Could not open file C:/Phil/CEL files Fibro alone/FANC Fibro/fibro PD331neo01.CEL > data2 <- gcrma(data1) Error: Object "data1" not found Error in probeNames(object) : Unable to find the argument "object" in selecting a method for function "probeNames" > exprs2excel(data2, file="Fibroalone_gcrma.csv and in addition, the CEL file is no more present in the folder as if it was deleted...! Any suggestion ? Thanks Philippe _______________________________________________ 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
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This bug is now fixed (as of affy 1.4.3). You'll have to wait for the overnight builds to go through to use it. As noted, don't use affy 1.4.2 for reading text cel files on windows, it does seem to like to delete cel files. Ben On Tue, 2003-12-02 at 06:09, James MacDonald wrote: > Correction: There is a bug in the Win32 version of affy 1.4.2. The *nix > version appears to work fine for text .cel files. > > > > 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 > > >>> "James MacDonald" <jmacdon@med.umich.edu> 12/02/03 09:01AM >>> > It appears that there is a bug in 1.4.2 that causes it to not read > text > .cel files. For now, I would recommend reverting to the release > version > for non-binary .cel files. > > 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 > > >>> <phguardiol@aol.com> 12/02/03 04:51AM >>> > Hi all, > I m trying to use Affy 1.4.2 with U133A chips on a new PC P4 with XP > Pro and R 1.8.1 > I m selecting the right Folder first where my CEL files are and then > paste on the command line: > data1 <- ReadAffy() > data2 <- gcrma(data1) > exprs2excel(data2, file="Fibroalone_gcrma.csv") > > then I obtain the following: > > library(affy) > Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. > > Synching your local package management information ... > Packages which have been added/updated: > matchprobes > arrayMagic > externalVector > limma > > > > library(gcrma) > Loading required package: MASS > > data1 <- ReadAffy() > Error in initialize(value, ...) : Could not open file C:/Phil/CEL > files > Fibro alone/FANC Fibro/fibro PD331neo01.CEL > > data2 <- gcrma(data1) > Error: Object "data1" not found > Error in probeNames(object) : Unable to find the argument "object" in > selecting a method for function "probeNames" > > exprs2excel(data2, file="Fibroalone_gcrma.csv > > and in addition, the CEL file is no more present in the folder as if > it > was deleted...! > Any suggestion ? > Thanks > Philippe > > _______________________________________________ > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu> http://www.stat.berkeley.edu/~bolstad
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@david-lapointe-225
Last seen 10.3 years ago
How can I tell what version I have? I loaded the devel version today but it cannot read the non-compressed CEL and deletes them, so it must not be the freshest. David > -----Original Message----- > From: James MacDonald [mailto:jmacdon@med.umich.edu] > Sent: Tuesday, December 02, 2003 9:09 AM > To: Phguardiol@aol.com; jmacdon@med.umich.edu; > bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] affy package problem > > > Correction: There is a bug in the Win32 version of affy > 1.4.2. The *nix version appears to work fine for text .cel files. > > > > 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 > > >>> "James MacDonald" <jmacdon@med.umich.edu> 12/02/03 09:01AM >>> > It appears that there is a bug in 1.4.2 that causes it to not > read text .cel files. For now, I would recommend reverting to > the release version for non-binary .cel files. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo> /bioconductor >
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> How can I tell what version I have? I loaded the devel version today but > it cannot read the non-compressed > CEL and deletes them, so it must not be the freshest. > package.description("affy")["Version"] Version #1.4.3 is the latest version and is currently on the website - you might have checked before it got updated. -J
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A.J. Rossini ▴ 810
@aj-rossini-209
Last seen 10.3 years ago
library(help=affy) # in general, library(help=PackageName) will provide the version information and more. "Lapointe, David" <david.lapointe@umassmed.edu> writes: > How can I tell what version I have? I loaded the devel version today but > it cannot read the non-compressed > CEL and deletes them, so it must not be the freshest. > > David > >> -----Original Message----- >> From: James MacDonald [mailto:jmacdon@med.umich.edu] >> Sent: Tuesday, December 02, 2003 9:09 AM >> To: Phguardiol@aol.com; jmacdon@med.umich.edu; >> bioconductor@stat.math.ethz.ch >> Subject: Re: [BioC] affy package problem >> >> >> Correction: There is a bug in the Win32 version of affy >> 1.4.2. The *nix version appears to work fine for text .cel files. >> >> >> >> 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 >> >> >>> "James MacDonald" <jmacdon@med.umich.edu> 12/02/03 09:01AM >>> >> It appears that there is a bug in 1.4.2 that causes it to not >> read text .cel files. For now, I would recommend reverting to >> the release version for non-binary .cel files. >> >> _______________________________________________ >> 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 > -- rossini@u.washington.edu http://www.analytics.washington.edu/ Biomedical and Health Informatics University of Washington Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email CONFIDENTIALITY NOTICE: This e-mail message and any attachme...{{dropped}}
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