S4 object??
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Wendy Chen ▴ 40
@wendy-chen-3748
Last seen 9.6 years ago
Hi all, I have loaded the LIMMA and Biobase package and tried these commands: library(limma) library("Biobase") data <- read.table("c:/temp/data.txt",header=T,row.names=1) ExpressionData <- as.matrix(data[,c(2,3,4,6,7,8)]) eset <- new("ExpressionSet", exprs = ExpressionData) design <- cbind(WT=1,P=c(0,1,1,0,1,1),G=c(0,1,0,0,1,0)) fit <- lmFit(eset,design) But I keep getting an eroor message after "lmFit" that says: Error in possibleExtends(cl, class2, class1Def, class2Def) : trying to get slot "subclasses" from an object (class "classRepresentation") that is not an S4 object I am using R-2.9.2. Whats happening now? I have done exactly the same commands in another computer and it works fine. I forgot which R version it was. But after installing the latest version nothing works. Pls advice... Regards, Wendy [[alternative HTML version deleted]]
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@james-w-macdonald-5106
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Hi Wendy, Wendy Chen wrote: > Hi all, > > > I have loaded the LIMMA and Biobase package and tried these commands: > > > library(limma) library("Biobase") data <- > read.table("c:/temp/data.txt",header=T,row.names=1) ExpressionData <- > as.matrix(data[,c(2,3,4,6,7,8)]) eset <- new("ExpressionSet", exprs = > ExpressionData) design <- > cbind(WT=1,P=c(0,1,1,0,1,1),G=c(0,1,0,0,1,0)) fit <- > lmFit(eset,design) > > But I keep getting an eroor message after "lmFit" that says: Error in > possibleExtends(cl, class2, class1Def, class2Def) : trying to get > slot "subclasses" from an object (class "classRepresentation") that > is not an S4 object > > I am using R-2.9.2. Whats happening now? I have done exactly the same > commands in another computer and it works fine. I forgot which R > version it was. But after installing the latest version nothing > works. Pls advice... I'm not sure why you get that error, but I would imagine it has something to do with the ExpressionSet you are creating. Note that limma will take any number of objects as input, including a matrix, so you don't need to create an ExpressionSet anyway. Usage: lmFit(object,design=NULL,ndups=1,spacing=1,block=NULL,correlation,weig hts=NULL,method="ls",...) Arguments: object: object of class 'numeric', 'matrix', 'MAList', 'EList', 'marrayNorm', 'ExpressionSet' or 'PLMset' containing log-ratios or log-values of expression for a series of microarrays Best, Jim > > Regards, Wendy > > > > [[alternative HTML version deleted]] > > > > -------------------------------------------------------------------- ---- > > > _______________________________________________ Bioconductor mailing > list Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
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Hi Jim, Even without creating the ExpressionSet I get the same error at the lmFit step: library(limma) library("Biobase") data <- read.table("c:/temp/data.txt",header=T,row.names=1) ExpressionData <- as.matrix(data[,c(2,3,4,6,7,8)]) design <-cbind(WT=1,P=c(0,1,1,0,1,1),G=c(0,1,0,0,1,0)) fit <-lmFit(eset,design) Error in possibleExtends(cl, class2, class1Def, class2Def) :     trying to get slot "subclasses" from an object (class "classRepresentation") that is not an S4 object I am suspecting I did not install something properly as I have done all those commands before changing to a new computer and it all worked fine. I have since tried re-installing everything but nothing works. Any idea what does that error message mean? Regards, Wendy ________________________________ From: James W. MacDonald <jmacdon@med.umich.edu> Cc: bioconductor@stat.math.ethz.ch Sent: Thu, October 22, 2009 9:12:09 PM Subject: Re: [BioC] S4 object?? Hi Wendy, Wendy Chen wrote: > Hi all, > > > I have loaded the LIMMA and Biobase package and tried these commands: > > > library(limma) library("Biobase") data <- > read.table("c:/temp/data.txt",header=T,row.names=1) ExpressionData <- > as.matrix(data[,c(2,3,4,6,7,8)]) eset <- new("ExpressionSet", exprs = > ExpressionData) design <- > cbind(WT=1,P=c(0,1,1,0,1,1),G=c(0,1,0,0,1,0)) fit <- > lmFit(eset,design) > > But I keep getting an eroor message after "lmFit" that says: Error in > possibleExtends(cl, class2, class1Def, class2Def) : trying to get > slot "subclasses" from an object (class "classRepresentation") that > is not an S4 object > > I am using R-2.9.2. Whats happening now? I have done exactly the same > commands in another computer and it works fine. I forgot which R > version it was. But after installing the latest version nothing > works. Pls advice... I'm not sure why you get that error, but I would imagine it has something to do with the ExpressionSet you are creating. Note that limma will take any number of objects as input, including a matrix, so you don't need to create an ExpressionSet anyway. Usage: lmFit(object,design=NULL,ndups=1,spacing=1,block=NULL,correlation,weig hts=NULL,method="ls",...) Arguments:   object: object of class 'numeric', 'matrix', 'MAList', 'EList',           'marrayNorm', 'ExpressionSet' or 'PLMset' containing           log-ratios or log-values of expression for a series of           microarrays Best, Jim > > Regards, Wendy > > > > [[alternative HTML version deleted]] > > > > -------------------------------------------------------------------- ---- > > > _______________________________________________ Bioconductor mailing > list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 [[alternative HTML version deleted]]
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On Thu, Oct 22, 2009 at 9:27 AM, Wendy Chen <wenehc@yahoo.com.sg> wrote: > Hi Jim, > > Even without creating the ExpressionSet I get the same error at the lmFit > step: > > library(limma) > library("Biobase") > data <- read.table("c:/temp/data.txt",header=T,row.names=1) > ExpressionData <- as.matrix(data[,c(2,3,4,6,7,8)]) > design <-cbind(WT=1,P=c(0,1,1,0,1,1),G=c(0,1,0,0,1,0)) > fit <-lmFit(eset,design) > > You are still using "eset". You want to use: fit <- lmFit(ExpressionData,design) Sean > Error in possibleExtends(cl, class2, class1Def, class2Def) : > trying to get slot "subclasses" from an object (class > "classRepresentation") that is not an S4 object > > > I am suspecting I did not install something properly as I have done all > those commands before changing to a new computer and it all worked fine. I > have since tried re-installing everything but nothing works. Any idea what > does that error message mean? > > Regards, > Wendy > > > > > > > ________________________________ > From: James W. MacDonald <jmacdon@med.umich.edu> > > Cc: bioconductor@stat.math.ethz.ch > Sent: Thu, October 22, 2009 9:12:09 PM > Subject: Re: [BioC] S4 object?? > > Hi Wendy, > > Wendy Chen wrote: > > Hi all, > > > > > > I have loaded the LIMMA and Biobase package and tried these commands: > > > > > > library(limma) library("Biobase") data <- > > read.table("c:/temp/data.txt",header=T,row.names=1) ExpressionData <- > > as.matrix(data[,c(2,3,4,6,7,8)]) eset <- new("ExpressionSet", exprs = > > ExpressionData) design <- > > cbind(WT=1,P=c(0,1,1,0,1,1),G=c(0,1,0,0,1,0)) fit <- > > lmFit(eset,design) > > > > But I keep getting an eroor message after "lmFit" that says: Error in > > possibleExtends(cl, class2, class1Def, class2Def) : trying to get > > slot "subclasses" from an object (class "classRepresentation") that > > is not an S4 object > > > > I am using R-2.9.2. Whats happening now? I have done exactly the same > > commands in another computer and it works fine. I forgot which R > > version it was. But after installing the latest version nothing > > works. Pls advice... > > I'm not sure why you get that error, but I would imagine it has something > to do with the ExpressionSet you are creating. Note that limma will take any > number of objects as input, including a matrix, so you don't need to create > an ExpressionSet anyway. > > Usage: > > > > lmFit(object,design=NULL,ndups=1,spacing=1,block=NULL,correlation,we ights=NULL,method="ls",...) > > Arguments: > > object: object of class 'numeric', 'matrix', 'MAList', 'EList', > 'marrayNorm', 'ExpressionSet' or 'PLMset' containing > log-ratios or log-values of expression for a series of > microarrays > > Best, > > Jim > > > > > > > Regards, Wendy > > > > > > > > [[alternative HTML version deleted]] > > > > > > > > ------------------------------------------------------------------ ------ > > > > > > _______________________________________________ Bioconductor mailing > > list Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > > archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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What is the output from sessionInfo(), and what do you get if you run traceback() right after the error? Jim Wendy Chen wrote: > Hi Jim, > > Even without creating the ExpressionSet I get the same error at the > lmFit step: > > library(limma) > library("Biobase") > data <- read.table("c:/temp/data.txt",header=T,row.names=1) > ExpressionData <- as.matrix(data[,c(2,3,4,6,7,8)]) > design <-cbind(WT=1,P=c(0,1,1,0,1,1),G=c(0,1,0,0,1,0)) > fit <-lmFit(eset,design) > Error in possibleExtends(cl, class2, class1Def, class2Def) : > trying to get slot "subclasses" from an object (class > "classRepresentation") that is not an S4 object > > I am suspecting I did not install something properly as I have done all > those commands before changing to a new computer and it all worked fine. > I have since tried re-installing everything but nothing works. Any idea > what does that error message mean? > > Regards, > Wendy > > <http: punni3.blogspot.com=""/> > > > -------------------------------------------------------------------- ---- > *From:* James W. MacDonald <jmacdon at="" med.umich.edu=""> > *To:* Wendy Chen <wenehc at="" yahoo.com.sg=""> > *Cc:* bioconductor at stat.math.ethz.ch > *Sent:* Thu, October 22, 2009 9:12:09 PM > *Subject:* Re: [BioC] S4 object?? > > Hi Wendy, > > Wendy Chen wrote: > > Hi all, > > > > > > I have loaded the LIMMA and Biobase package and tried these commands: > > > > > > library(limma) library("Biobase") data <- > > read.table("c:/temp/data.txt",header=T,row.names=1) ExpressionData <- > > as.matrix(data[,c(2,3,4,6,7,8)]) eset <- new("ExpressionSet", exprs = > > ExpressionData) design <- > > cbind(WT=1,P=c(0,1,1,0,1,1),G=c(0,1,0,0,1,0)) fit <- > > lmFit(eset,design) > > > > But I keep getting an eroor message after "lmFit" that says: Error in > > possibleExtends(cl, class2, class1Def, class2Def) : trying to get > > slot "subclasses" from an object (class "classRepresentation") that > > is not an S4 object > > > > I am using R-2.9.2. Whats happening now? I have done exactly the same > > commands in another computer and it works fine. I forgot which R > > version it was. But after installing the latest version nothing > > works. Pls advice... > > I'm not sure why you get that error, but I would imagine it has > something to do with the ExpressionSet you are creating. Note that limma > will take any number of objects as input, including a matrix, so you > don't need to create an ExpressionSet anyway. > > Usage: > > > lmFit(object,design=NULL,ndups=1,spacing=1,block=NULL,correlation,we ights=NULL,method="ls",...) > > > Arguments: > > object: object of class 'numeric', 'matrix', 'MAList', 'EList', > 'marrayNorm', 'ExpressionSet' or 'PLMset' containing > log-ratios or log-values of expression for a series of > microarrays > > Best, > > Jim > > > > > > > Regards, Wendy > > > > > > > > [[alternative HTML version deleted]] > > > > > > > > ----------------------------------------------------------------- ------- > > > > > > _______________________________________________ Bioconductor mailing > > list Bioconductor at stat.math.ethz.ch > <mailto:bioconductor at="" stat.math.ethz.ch=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > > archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
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>From sessionInfo() and traceback(), I get > sessionInfo() R version 2.9.2 (2009-08-24) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats���� graphics� grDevices utils���� datasets� methods�� base���� other attached packages: [1] limma_1.9.0�� Biobase_2.4.1 > traceback() No traceback available � � ________________________________ From: James W. MacDonald <jmacdon@med.umich.edu> Cc: bioconductor@stat.math.ethz.ch Sent: Thu, October 22, 2009 9:31:24 PM Subject: Re: [BioC] S4 object?? What is the output from sessionInfo(), and what do you get if you run traceback() right after the error? Jim Wendy Chen wrote: > Hi Jim, >� Even without creating the ExpressionSet I get the same error at the lmFit step: >� library(limma) > library("Biobase") > data <- read.table("c:/temp/data.txt",header=T,row.names=1) > ExpressionData <- as.matrix(data[,c(2,3,4,6,7,8)]) > design <-cbind(WT=1,P=c(0,1,1,0,1,1),G=c(0,1,0,0,1,0)) > fit <-lmFit(eset,design) > Error in possibleExtends(cl, class2, class1Def, class2Def) : >� � trying to get slot "subclasses" from an object (class "classRepresentation") that is not an S4 object >� I am suspecting I did not install something properly as I have done all those commands before changing to a new computer and it all worked fine. I have since tried re-installing everything but nothing works. Any idea what does that error message mean? >� Regards, > Wendy >� <http: punni3.blogspot.com=""/> > > -------------------------------------------------------------------- ---- > *From:* James W. MacDonald <jmacdon@med.umich.edu> > *Cc:* bioconductor@stat.math.ethz.ch > *Sent:* Thu, October 22, 2009 9:12:09 PM > *Subject:* Re: [BioC] S4 object?? > > Hi Wendy, > > Wendy Chen wrote: >� > Hi all, >� > >� > >� > I have loaded the LIMMA and Biobase package and tried these commands: >� > >� > >� > library(limma) library("Biobase") data <- >� > read.table("c:/temp/data.txt",header=T,row.names=1) ExpressionData <- >� > as.matrix(data[,c(2,3,4,6,7,8)]) eset <- new("ExpressionSet", exprs = >� > ExpressionData) design <- >� > cbind(WT=1,P=c(0,1,1,0,1,1),G=c(0,1,0,0,1,0)) fit <- >� > lmFit(eset,design) >� > >� > But I keep getting an eroor message after "lmFit" that says: Error in >� > possibleExtends(cl, class2, class1Def, class2Def) : trying to get >� > slot "subclasses" from an object (class "classRepresentation") that >� > is not an S4 object >� > >� > I am using R-2.9.2. Whats happening now? I have done exactly the same >� > commands in another computer and it works fine. I forgot which R >� > version it was. But after installing the latest version nothing >� > works. Pls advice... > > I'm not sure why you get that error, but I would imagine it has something to do with the ExpressionSet you are creating. Note that limma will take any number of objects as input, including a matrix, so you don't need to create an ExpressionSet anyway. > > Usage: > > > lmFit(object,design=NULL,ndups=1,spacing=1,block=NULL,correlation,we ights=NULL,method="ls",...) > > Arguments: > >� object: object of class 'numeric', 'matrix', 'MAList', 'EList', >� � � � � 'marrayNorm', 'ExpressionSet' or 'PLMset' containing >� � � � � log-ratios or log-values of expression for a series of >� � � � � microarrays > > Best, > > Jim > > > >� > >� > Regards, Wendy >� > >� > >� > >� > [[alternative HTML version deleted]] >� > >� > >� > >� > ----------------------------------------------------------------- ------- >� > >� > >� > _______________________________________________ Bioconductor mailing >� > list Bioconductor@stat.math.ethz.ch <mailto:bioconductor@stat.math.ethz.ch> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the >� > archives: >� > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 [[alternative HTML version deleted]]
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Your packages are out of date. Try updating packages following insructructions at http://bIoconductor.org/install -- Martin Morgan On Oct 22, 2009, at 5:25 PM, Wendy Chen <wenehc at="" yahoo.com.sg=""> wrote: >> From sessionInfo() and traceback(), I get > >> sessionInfo() > R version 2.9.2 (2009-08-24) > i386-pc-mingw32 > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States. > 1252;LC_MONETARY=English_United States. > 1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] limma_1.9.0 Biobase_2.4.1 >> traceback() > No traceback available > > > > > > > > ________________________________ > From: James W. MacDonald <jmacdon at="" med.umich.edu=""> > > Cc: bioconductor at stat.math.ethz.ch > Sent: Thu, October 22, 2009 9:31:24 PM > Subject: Re: [BioC] S4 object?? > > What is the output from sessionInfo(), and what do you get if you > run traceback() right after the error? > > Jim > > > > Wendy Chen wrote: >> Hi Jim, >> Even without creating the ExpressionSet I get the same error at >> the lmFit step: >> library(limma) >> library("Biobase") >> data <- read.table("c:/temp/data.txt",header=T,row.names=1) >> ExpressionData <- as.matrix(data[,c(2,3,4,6,7,8)]) >> design <-cbind(WT=1,P=c(0,1,1,0,1,1),G=c(0,1,0,0,1,0)) >> fit <-lmFit(eset,design) >> Error in possibleExtends(cl, class2, class1Def, class2Def) : >> trying to get slot "subclasses" from an object (class >> "classRepresentation") that is not an S4 object >> I am suspecting I did not install something properly as I have >> done all those commands before changing to a new computer and it >> all worked fine. I have since tried re-installing everything but >> nothing works. Any idea what does that error message mean? >> Regards, >> Wendy >> <http: punni3.blogspot.com=""/> >> >> --- >> --------------------------------------------------------------------- >> *From:* James W. MacDonald <jmacdon at="" med.umich.edu=""> > >> *Cc:* bioconductor at stat.math.ethz.ch >> *Sent:* Thu, October 22, 2009 9:12:09 PM >> *Subject:* Re: [BioC] S4 object?? >> >> Hi Wendy, >> >> Wendy Chen wrote: >> > Hi all, >> > >> > >> > I have loaded the LIMMA and Biobase package and tried these >> commands: >> > >> > >> > library(limma) library("Biobase") data <- >> > read.table("c:/temp/data.txt",header=T,row.names=1) >> ExpressionData <- >> > as.matrix(data[,c(2,3,4,6,7,8)]) eset <- new("ExpressionSet", >> exprs = >> > ExpressionData) design <- >> > cbind(WT=1,P=c(0,1,1,0,1,1),G=c(0,1,0,0,1,0)) fit <- >> > lmFit(eset,design) >> > >> > But I keep getting an eroor message after "lmFit" that says: >> Error in >> > possibleExtends(cl, class2, class1Def, class2Def) : trying to get >> > slot "subclasses" from an object (class "classRepresentation") >> that >> > is not an S4 object >> > >> > I am using R-2.9.2. Whats happening now? I have done exactly >> the same >> > commands in another computer and it works fine. I forgot which R >> > version it was. But after installing the latest version nothing >> > works. Pls advice... >> >> I'm not sure why you get that error, but I would imagine it has >> something to do with the ExpressionSet you are creating. Note that >> limma will take any number of objects as input, including a matrix, >> so you don't need to create an ExpressionSet anyway. >> >> Usage: >> >> >> lmFit >> (object, >> design= >> NULL, >> ndups= >> 1,spacing=1,block=NULL,correlation,weights=NULL,method="ls",...) >> >> Arguments: >> >> object: object of class 'numeric', 'matrix', 'MAList', 'EList', >> 'marrayNorm', 'ExpressionSet' or 'PLMset' containing >> log-ratios or log-values of expression for a series of >> microarrays >> >> Best, >> >> Jim >> >> >> >> > >> > Regards, Wendy >> > >> > >> > >> > [[alternative HTML version deleted]] >> > >> > >> > >> > >> --- >> --------------------------------------------------------------------- >> > >> > >> > _______________________________________________ Bioconductor >> mailing >> > list Bioconductor at stat.math.ethz.ch <mailto:bioconductor at="" stat.math.ethz.ch="">> > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the >> > archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> -- James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> > > -- James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Jim, I tried with an older version of R, i.e., R-2.4.1 and it all worked now. I cant explain why. But guess I'll just stick to the older version for now. Thanks Wendy ________________________________ From: James W. MacDonald <jmacdon@med.umich.edu> Cc: bioconductor@stat.math.ethz.ch Sent: Thu, October 22, 2009 9:31:24 PM Subject: Re: [BioC] S4 object?? What is the output from sessionInfo(), and what do you get if you run traceback() right after the error? Jim Wendy Chen wrote: > Hi Jim, >  Even without creating the ExpressionSet I get the same error at the lmFit step: >  library(limma) > library("Biobase") > data <- read.table("c:/temp/data.txt",header=T,row.names=1) > ExpressionData <- as.matrix(data[,c(2,3,4,6,7,8)]) > design <-cbind(WT=1,P=c(0,1,1,0,1,1),G=c(0,1,0,0,1,0)) > fit <-lmFit(eset,design) > Error in possibleExtends(cl, class2, class1Def, class2Def) : >    trying to get slot "subclasses" from an object (class "classRepresentation") that is not an S4 object >  I am suspecting I did not install something properly as I have done all those commands before changing to a new computer and it all worked fine. I have since tried re-installing everything but nothing works. Any idea what does that error message mean? >  Regards, > Wendy > > -------------------------------------------------------------------- ---- > *From:* James W. MacDonald <jmacdon@med.umich.edu> > *Cc:* bioconductor@stat.math.ethz.ch > *Sent:* Thu, October 22, 2009 9:12:09 PM > *Subject:* Re: [BioC] S4 object?? > > Hi Wendy, > > Wendy Chen wrote: >  > Hi all, >  > >  > >  > I have loaded the LIMMA and Biobase package and tried these commands: >  > >  > >  > library(limma) library("Biobase") data <- >  > read.table("c:/temp/data.txt",header=T,row.names=1) ExpressionData <- >  > as.matrix(data[,c(2,3,4,6,7,8)]) eset <- new("ExpressionSet", exprs = >  > ExpressionData) design <- >  > cbind(WT=1,P=c(0,1,1,0,1,1),G=c(0,1,0,0,1,0)) fit <- >  > lmFit(eset,design) >  > >  > But I keep getting an eroor message after "lmFit" that says: Error in >  > possibleExtends(cl, class2, class1Def, class2Def) : trying to get >  > slot "subclasses" from an object (class "classRepresentation") that >  > is not an S4 object >  > >  > I am using R-2.9.2. Whats happening now? I have done exactly the same >  > commands in another computer and it works fine. I forgot which R >  > version it was. But after installing the latest version nothing >  > works. Pls advice... > > I'm not sure why you get that error, but I would imagine it has something to do with the ExpressionSet you are creating. Note that limma will take any number of objects as input, including a matrix, so you don't need to create an ExpressionSet anyway. > > Usage: > > > lmFit(object,design=NULL,ndups=1,spacing=1,block=NULL,correlation,we ights=NULL,method="ls",...) > > Arguments: > >  object: object of class 'numeric', 'matrix', 'MAList', 'EList', >          'marrayNorm', 'ExpressionSet' or 'PLMset' containing >          log-ratios or log-values of expression for a series of >          microarrays > > Best, > > Jim > > > >  > >  > Regards, Wendy >  > >  > >  > >  > [[alternative HTML version deleted]] >  > >  > >  > >  > ----------------------------------------------------------------- ------- >  > >  > >  > _______________________________________________ Bioconductor mailing >  > list Bioconductor@stat.math.ethz.ch <mailto:bioconductor@stat.math.ethz.ch> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the >  > archives: >  > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 [[alternative HTML version deleted]]
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