Question: S4 object??
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gravatar for Wendy Chen
9.8 years ago by
Wendy Chen40
Wendy Chen40 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... Regards, Wendy [[alternative HTML version deleted]]
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ADD COMMENTlink modified 9.8 years ago by James W. MacDonald50k • written 9.8 years ago by Wendy Chen40
Answer: S4 object??
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gravatar for James W. MacDonald
9.8 years ago by
United States
James W. MacDonald50k wrote:
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
ADD COMMENTlink written 9.8 years ago by James W. MacDonald50k
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]]
ADD REPLYlink written 9.8 years ago by Wendy Chen40
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]]
ADD REPLYlink written 9.8 years ago by Sean Davis21k
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
ADD REPLYlink written 9.8 years ago by James W. MacDonald50k
>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]]
ADD REPLYlink written 9.8 years ago by Wendy Chen40
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
ADD REPLYlink written 9.8 years ago by Martin Morgan ♦♦ 23k
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]]
ADD REPLYlink written 9.8 years ago by Wendy Chen40
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