Error message when trying to ReadAffy with widgets function: help, please?

Error message when trying to ReadAffy with widgets function: help, please?_Part 2

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John Zhang ★ 2.9k

@john-zhang-6

Last seen 10.3 years ago

>But when I try the widget option I still get: > >> alldata <- ReadAffy(widget=TRUE) >Error in structure(.External("dotTcl", ..., PACKAGE = "tcltk"), class = >"tclObj") : > [tcl] ambiguous option "-col": must be -column, -columnspan, >-in, -ipadx, -ipady, -padx, -pady, -row, -rowspan, or -sticky Try to get/install the latest version of tkWidgets 1.1.18 and see what happens. > >May this have anything to do with the environment variable set up for >Tcl/Tk? > >I have it as follows: > >Variable name: TCL_LIBRARY > >Variable value: c:\tcl\lib\tcl8.4. The setting is correct. > >Thanks again for all your suggestions, >Fatima > > > >_______ >? > >? >F?tima N??ez, PhD >Centre for Cancer Research (CIC) >University of Salamanca-CSIC >Campus Unamuno >37007 Salamanca?????????????????????????????????????????????????? >Spain >Phone: + 34 923 294802 >Fax:?????+ 34 923 294743 >E-mail: fnunez@usal.es > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

Cancer tkWidgets Cancer tkWidgets • 1.6k views

ADD COMMENT • link updated 21.6 years ago by Isaac Neuhaus ▴ 360 • written 21.6 years ago by John Zhang ★ 2.9k

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Isaac Neuhaus ▴ 360

@isaac-neuhaus-22

Last seen 9.6 years ago

United States

I am running R 1.6.2 with affy 1.2.22 and I am getting the following error: > cels<-list() > cels[1] <- "GM1A.cel" > cels[2] <- "GM2A.cel" > cels[3] <- "GM3A.cel" > cels[4] <- "GM4A.cel" > cels[5] <- "GM5A.cel" > cels[6] <- "GM6A.cel" > cels[7] <- "GM7A.cel" > cels[8] <- "GM8A.cel" > cels[9] <- "GM9A.cel" > data <- ReadAffy(filenames=cels, verbose =T) 1 reading GM2001041001A.cel ...done. instanciating an AffyBatch (intensity a 409600x9 matrix)...done. Error in "intensity<-"(*tmp*, value = c(intensity(cel))) : couldn't find function "exprs<-" > > traceback() 3: "intensity<-"(*tmp*, value = c(intensity(cel))) 2: read.affybatch(filenames = filenames, phenoData = phenoData, description = description, notes = notes, compress = compress, rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, verbose = verbose) 1: ReadAffy(filenames = cels, verbose = T) > What should I do? Thanks in advance, Isaac

ADD COMMENT • link 21.6 years ago Isaac Neuhaus ▴ 360

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how about Biobase? you may need to upgrade Biobase to the latest. -r On Tue, 27 May 2003, Isaac Neuhaus wrote: > I am running R 1.6.2 with affy 1.2.22 and I am getting the following error: > > > cels<-list() > > cels[1] <- "GM1A.cel" > > cels[2] <- "GM2A.cel" > > cels[3] <- "GM3A.cel" > > cels[4] <- "GM4A.cel" > > cels[5] <- "GM5A.cel" > > cels[6] <- "GM6A.cel" > > cels[7] <- "GM7A.cel" > > cels[8] <- "GM8A.cel" > > cels[9] <- "GM9A.cel" > > data <- ReadAffy(filenames=cels, verbose =T) > 1 reading GM2001041001A.cel ...done. > instanciating an AffyBatch (intensity a 409600x9 matrix)...done. > Error in "intensity<-"(*tmp*, value = c(intensity(cel))) : > couldn't find function "exprs<-" > > > > traceback() > 3: "intensity<-"(*tmp*, value = c(intensity(cel))) > 2: read.affybatch(filenames = filenames, phenoData = phenoData, > description = description, notes = notes, compress = compress, > rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, > verbose = verbose) > 1: ReadAffy(filenames = cels, verbose = T) > > > > What should I do? > > Thanks in advance, > > Isaac > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

ADD REPLY • link 21.6 years ago Rafael A. Irizarry ★ 2.3k

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I have Biobase version 1.1.3. I Rafael A. Irizarry wrote: >how about Biobase? you may need to upgrade Biobase to the latest. >-r >On Tue, 27 May 2003, >Isaac Neuhaus wrote: > > > >>I am running R 1.6.2 with affy 1.2.22 and I am getting the following error: >> >> > cels<-list() >> > cels[1] <- "GM1A.cel" >> > cels[2] <- "GM2A.cel" >> > cels[3] <- "GM3A.cel" >> > cels[4] <- "GM4A.cel" >> > cels[5] <- "GM5A.cel" >> > cels[6] <- "GM6A.cel" >> > cels[7] <- "GM7A.cel" >> > cels[8] <- "GM8A.cel" >> > cels[9] <- "GM9A.cel" >> > data <- ReadAffy(filenames=cels, verbose =T) >>1 reading GM2001041001A.cel ...done. >>instanciating an AffyBatch (intensity a 409600x9 matrix)...done. >>Error in "intensity<-"(*tmp*, value = c(intensity(cel))) : >> couldn't find function "exprs<-" >> > >> > traceback() >>3: "intensity<-"(*tmp*, value = c(intensity(cel))) >>2: read.affybatch(filenames = filenames, phenoData = phenoData, >> description = description, notes = notes, compress = compress, >> rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, >> verbose = verbose) >>1: ReadAffy(filenames = cels, verbose = T) >> > >> >>What should I do? >> >>Thanks in advance, >> >>Isaac >> >>_______________________________________________ >>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 > >

ADD REPLY • link 21.6 years ago Isaac Neuhaus ▴ 360

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So it's more than time to update... (as adviced when you do 'library(affy)') L. On Tue, May 27, 2003 at 03:15:58PM -0400, Isaac Neuhaus wrote: > I have Biobase version 1.1.3. > > I > > Rafael A. Irizarry wrote: > > >how about Biobase? you may need to upgrade Biobase to the latest. > >-r > >On Tue, 27 May 2003, > >Isaac Neuhaus wrote: > > > > > > > >>I am running R 1.6.2 with affy 1.2.22 and I am getting the following > >>error: > >> > >>> cels<-list() > >>> cels[1] <- "GM1A.cel" > >>> cels[2] <- "GM2A.cel" > >>> cels[3] <- "GM3A.cel" > >>> cels[4] <- "GM4A.cel" > >>> cels[5] <- "GM5A.cel" > >>> cels[6] <- "GM6A.cel" > >>> cels[7] <- "GM7A.cel" > >>> cels[8] <- "GM8A.cel" > >>> cels[9] <- "GM9A.cel" > >>> data <- ReadAffy(filenames=cels, verbose =T) > >>1 reading GM2001041001A.cel ...done. > >>instanciating an AffyBatch (intensity a 409600x9 matrix)...done. > >>Error in "intensity<-"(*tmp*, value = c(intensity(cel))) : > >> couldn't find function "exprs<-" > >>> > >>> traceback() > >>3: "intensity<-"(*tmp*, value = c(intensity(cel))) > >>2: read.affybatch(filenames = filenames, phenoData = phenoData, > >> description = description, notes = notes, compress = compress, > >> rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, > >> verbose = verbose) > >>1: ReadAffy(filenames = cels, verbose = T) > >>> > >> > >>What should I do? > >> > >>Thanks in advance, > >> > >>Isaac > >> > >>_______________________________________________ > >>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 -- -------------------------------------------------------------- currently at the National Yang-Ming University in Taipei, Taiwan -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent

ADD REPLY • link 21.6 years ago Laurent Gautier ★ 2.3k

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I updated and it now it works. Thank you all. Isaac Laurent Gautier wrote: >So it's more than time to update... >(as adviced when you do 'library(affy)') > > >L. > > >On Tue, May 27, 2003 at 03:15:58PM -0400, Isaac Neuhaus wrote: > > >>I have Biobase version 1.1.3. >> >>I >> >>Rafael A. Irizarry wrote: >> >> >> >>>how about Biobase? you may need to upgrade Biobase to the latest. >>>-r >>>On Tue, 27 May 2003, >>>Isaac Neuhaus wrote: >>> >>> >>> >>> >>> >>>>I am running R 1.6.2 with affy 1.2.22 and I am getting the following >>>>error: >>>> >>>> >>>> >>>>>cels<-list() >>>>>cels[1] <- "GM1A.cel" >>>>>cels[2] <- "GM2A.cel" >>>>>cels[3] <- "GM3A.cel" >>>>>cels[4] <- "GM4A.cel" >>>>>cels[5] <- "GM5A.cel" >>>>>cels[6] <- "GM6A.cel" >>>>>cels[7] <- "GM7A.cel" >>>>>cels[8] <- "GM8A.cel" >>>>>cels[9] <- "GM9A.cel" >>>>>data <- ReadAffy(filenames=cels, verbose =T) >>>>> >>>>> >>>>1 reading GM2001041001A.cel ...done. >>>>instanciating an AffyBatch (intensity a 409600x9 matrix)...done. >>>>Error in "intensity<-"(*tmp*, value = c(intensity(cel))) : >>>> couldn't find function "exprs<-" >>>> >>>> >>>>>traceback() >>>>> >>>>> >>>>3: "intensity<-"(*tmp*, value = c(intensity(cel))) >>>>2: read.affybatch(filenames = filenames, phenoData = phenoData, >>>> description = description, notes = notes, compress = compress, >>>> rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, >>>> verbose = verbose) >>>>1: ReadAffy(filenames = cels, verbose = T) >>>> >>>> >>>>What should I do? >>>> >>>>Thanks in advance, >>>> >>>>Isaac >>>> >>>>_______________________________________________ >>>>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 >> >> > > >

ADD REPLY • link 21.6 years ago Isaac Neuhaus ▴ 360

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