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Hi Yuan, Please read the posting guide for this mailing list and follow the directions there, and especially provide the output of sessionInfo. I don't see any problems with these commands, so I suspect you have some issues with your installation. best wishes Robert Yuan Jian wrote: > Hello, > > I have struggled the following simple commands for long time, can you please fix the problem? > > > library("affydata") >> data(Dilution) >> pm(Dilution, "1001_at")[1:3, ] > Error in assayData(object) : > no slot of name "assayData" for this object of class "AffyBatch" > > Thanks > Yuan > > > > --------------------------------- > > [[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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

Hi Yuan -- A general procedure for updating packages is on the Bioconductor web site http://bioconductor.org/download, under 'Update packages': in a new R session (e.g., R --vanilla) > source('http://bioconductor.org/biocLite.R') > update.packages(repos=biocinstallRepos()) (add the argument ask=FALSE if you have many packages requiring update and trust that all will be updated correctly). As people are trying to be helpful and provide advice to you, I'll add a suggestion that an effective strategy for 'debugging' is to make things as simple as possible. So by the time I'm posting a question to this list my sessionInfo() will contain only the packages required to reproduce the problem (no need for 19 packages to demonstrate an out-of-date MLL.B!), and the example will be stripped to its barest minimum, e.g., your subsetting statement might be reduced to Data <- MLL.B[,1]. You (or others reading this post and following its advice) might discover in the process that the 'bug' is actually a simple typo, or not related to what it appeared to be, or otherwise resolve the issue. You'll also make it easier for those with experience to spot the problem, and hence offer a solution. Another resource is the Bioconductor mailing list archives and the search facilities (not altogether satisfactory, I admit), again linked from the Bioconductor home page. The problem of old Dilution data sets was common a year or so ago when most people transitioned from R 2.4 to 2.5 (I think; it might have been 2.3 to 2.4). Martin Yuan Jian <jayuan2008 at="" yahoo.com=""> writes: > Hi Kasper, > thank you very much. it worked. > another similar problem is > > > library("ALLMLL") >> data(MLL.B) > Warning message: > 'MLL.B' looks like a pre-2.4.0 S4 object: please recreate it >> Data <-MLL.B[,c(2,1,3:5,14,6,13)] > Error in MLL.B[, c(2, 1, 3:5, 14, 6, 13)] : > incorrect number of dimensions > > this command is from "Bioinformatics and Computational Biology Solutions using R and > Bioconductor" edited by R Gentleman, et. al > > can you please tell me how to "recreate MLL.B"? > > > sessionInfo() > R version 2.6.1 (2007-11-26) > i386-pc-mingw32 > locale: > LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC _MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australi a.1252 > attached base packages: > [1] tools stats graphics grDevices datasets utils methods base > other attached packages: > [1] ALLMLL_1.0 hgu95av2cdf_2.0.0 affydata_1.4.0 preprocessCore_1.0.0 affyio_1.6.1 > [6] Biobase_1.16.2 aroma.affymetrix_0.8.3 affy_1.16.0 aroma.apd_0.1.3 R.huge_0.1.5 > [11] digest_0.3.1 aroma.light_1.6.0 affxparser_1.10.2 R.rsp_0.3.3 R.cache_0.1.6 > [16] EBImage_2.2.0 R.utils_0.9.8 R.oo_1.4.1 R.methodsS3_1.0.0 >> > > > > Kasper Daniel Hansen <khansen at="" stat.berkeley.edu=""> wrote: > You might want to do an > Dilution = updateObject(Dilution) > my guess is that you are using a recent version of affy/Biobase with > an old version of the Dilution dataset. You could also just re- > install Dilution, that should fix it (assuming that you are running a > recent version of R etc) > > Kasper > > On Jan 23, 2008, at 9:43 PM, Yuan Jian wrote: > >> Hi Robert, >> thanks for your reply. I tried several time to reinstall >> packages, but failed to find solution. >> here is seeeionInfor: >>> sessionInfo() >> R version 2.6.1 (2007-11-26) >> i386-pc-mingw32 >> locale: >> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia. >> 1252;LC_MONETARY=English_Australia. >> 1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252 >> attached base packages: >> [1] tools stats graphics grDevices datasets utils >> methods base >> other attached packages: >> [1] hgu95av2cdf_2.0.0 affydata_1.4.0 >> preprocessCore_1.0.0 affyio_1.6.1 Biobase_1.16.2 >> [6] aroma.affymetrix_0.8.3 affy_1.16.0 >> aroma.apd_0.1.3 R.huge_0.1.5 digest_0.3.1 >> [11] aroma.light_1.6.0 affxparser_1.10.2 >> R.rsp_0.3.3 R.cache_0.1.6 EBImage_2.2.0 >> [16] R.utils_0.9.8 R.oo_1.4.1 R.methodsS3_1.0.0 >> >> >> >> Robert Gentleman wrote: >> Hi Yuan, >> Please read the posting guide for this mailing list and follow the >> directions there, and especially provide the output of sessionInfo. >> >> I don't see any problems with these commands, so I suspect you have >> some issues with your installation. >> >> best wishes >> Robert >> >> Yuan Jian wrote: >>> Hello, >>> >>> I have struggled the following simple commands for long time, can >>> you please fix the problem? >>> >>>> library("affydata") >>>> data(Dilution) >>>> pm(Dilution, "1001_at")[1:3, ] >>> Error in assayData(object) : >>> no slot of name "assayData" for this object of class "AffyBatch" >>> >>> Thanks >>> Yuan >>> >>> >>> >>> --------------------------------- >>> >>> [[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 >>> >> >> -- >> Robert Gentleman, PhD >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M2-B876 >> PO Box 19024 >> Seattle, Washington 98109-1024 >> 206-667-7700 >> rgentlem at fhcrc.org >> >> >> >> --------------------------------- >> >> [[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 > > > > > --------------------------------- > > [[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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793