With the show(obj) function and the write.table function, I can see the stuff in the old objects so that may solve the immediate problem But changing exprSet to ExpressionSet is attractive And I see it has been discussed before (see below) =========================== [BioC] Error loading, on Bioconductor 1.8, exprSet generated with bioconductor 1.7 Martin Morgan mtmorgan at fhcrc.org Thu Jun 8 18:11:14 CEST 2006 ? Previous message: [BioC] Error loading, on Bioconductor 1.8, exprSet generated with bioconductor 1.7 ? Next message: [BioC] [SPAM] Re: Error loading, on Bioconductor 1.8, exprSet generated with bioconductor 1.7 ? Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Hi Raf, Thanks for the clarification. It sounds like you've found a good solution. The long-term intention is to move away from exprSet as the basic building block, and toward a similar 'ExpressionSet' class. With this in mind, you could also have done (with the current version of Biobase) > obj <- as(tr7.rma, "ExpressionSet") to obtain an ExpressionSet from your (broken) exprSet. An ExpressionSet has methods like exprs(), phenoData(), and pData() that work as exprSet methods, so for many purposes having an ExpressionSet is a great replacement for exprSet. It's important to be able to return to previous versions of objects, and make them 'current'. To that end, the development version of Biobase introduces ways of 'versioning' objects (so that it's easy to figure out when the object was created) and an 'updateObject' method to bring an object up to date. So in the next release of Biobase (available to those already using the 'development' branch of R) you'll be able to > obj <- updateObject(tr76.rma) and stand a reasonable chance of getting an object that satisfies the current definition of exprSet. ============================================= So I try > ABeset_gcrmaExpressionSet <- as (ABeset_gcrma, "ExpressionSet") And get Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Warning message: In asMethod(object) : missing or mis-shaped 'se.exprs' in original object; creating ExpressionSet without se.exprs Then I try > ABeset_gcrmaUPDATE <- updateObject(ABeset_gcrma) And get Error in updateObjectFromSlots(object, ..., verbose = verbose) : could not updateObject to class 'phenoData' consider defining an 'updateObject' method for class 'phenoData' All with > sessionInfo() R version 2.8.0 Patched (2008-10-26 r46783) i386-apple-darwin9.5.0 locale: C attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] Biobase_2.2.0 > .Machine$sizeof.pointer [1] 8 Now since I can "see" the data with show and write.table I should probably quit, but for the fun of it, are either of these messages a "quick fix" for a novice? > > > > > > > > > From: Robert Gentleman <rgentlem at="" fhcrc.org=""> > Date: Tue, 28 Oct 2008 11:57:36 -0700 > To: Loren Engrav <engrav at="" u.washington.edu=""> > Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: Re: [BioC] Does old workspace work? > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Re the quality of the link: You need to ask the owner, not this list > > and the answer to your second question is that it depends on what you > want to catch up on. Ideally packages should have up to date vignettes, > and they are your main starting point. Contact maintainers if the > vignettes are incomplete or out of date. > > best wishes > Robert > > Loren Engrav wrote: >> Ok, I can deal with change >> >> One more question, to learn about and deal with the deprecated stuff >> >> Is the file at the url below current, or out of date? >> >> http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual. html#BioC >> primer >> >> If it is out of date, is there a better url to catch up fast? >> >>> From: Robert Gentleman <rgentlem at="" fhcrc.org=""> >>> Date: Tue, 28 Oct 2008 09:56:31 -0700 >>> To: Loren Engrav <engrav at="" u.washington.edu=""> >>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >>> Subject: Re: [BioC] Does old workspace work? >>> >> Loren Engrav wrote: >>>>> Ok, I will get my stuff modern >>>>> One more question >>>>> Those old saved workspaces and histories might be 32bit from before I went >>>>> to 64bit >>>>> If they are 32bit workspaces will they work in 64bit (save for the >>>>> deprecated stuff) >> Currently that is the case. But I am not sure how long it will remain >> so, as it means that R cannot be truly 64bit, so likely in the next year >> or so some change will be needed. Of course, one will always be able to >> read 32 bit workspaces in 64bits, but the converse will not likely hold >> for very much longer >> >> Robert >> >> >>>>> >>>>>> From: Robert Gentleman <rgentlem at="" fhcrc.org=""> >>>>>> Date: Mon, 27 Oct 2008 22:31:21 -0700 >>>>>> To: Loren Engrav <engrav at="" u.washington.edu=""> >>>>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >>>>>> Subject: Re: [BioC] Does old workspace work? >>>>>> >>>>>> Hi, >>>>>> >>>>>> Loren Engrav wrote: >>>>>>>> sessionInfo() >>>>>>> R version 2.8.0 Patched (2008-10-26 r46783) >>>>>>> i386-apple-darwin9.5.0 >>>>>>> >>>>>>> locale: >>>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>>>>> >>>>>>> attached base packages: >>>>>>> [1] splines tools stats graphics grDevices utils datasets >>>>>>> methods base >>>>>>> >>>>>>> other attached packages: >>>>>>> [1] simpleaffy_2.18.0 genefilter_1.22.0 survival_2.34-1 >>>>>>> affyio_1.10.0 >>>>>>> porcinecdf_2.3.0 gcrma_2.14.0 matchprobes_1.14.0 affy_1.20.0 >>>>>>> Biobase_2.2.0 >>>>>>> >>>>>>> loaded via a namespace (and not attached): >>>>>>> [1] AnnotationDbi_1.4.0 DBI_0.2-4 RSQLite_0.7-1 >>>>>>> annotate_1.20.0 preprocessCore_1.4.0 >>>>>>> >>>>>>> ============== >>>>>>> A year or so ago I ran 64bit R on Mac PPC and saved various workspaces >>>>>>> >>>>>>> Now am running 64bit R on Intel 2x3.2 QuadCore and MacOS 10.5.5 >>>>>>> >>>>>>> I load up the old workspaces >>>>>>> and I enter >>>>>>> >>>>>>>> write.exprs(ABeset_gcrma, file="ABeset_gcrma081028orig.txt") >>>>>>> Where ABeset_gcrma is an old file >>>>>>> >>>>>>> and I get >>>>>>> Error in function (classes, fdef, mtable) : >>>>>>> unable to find an inherited method for function "write.exprs", for >>>>>>> signature >>>>>>> "exprSet" >>>>>>> >>>>>> It was probably more than a year ago - the exprSet class was >>>>>> deprecated and subsequently made defunct. >>>>>> >>>>>> You could try to do: >>>>>> library(Biobase) >>>>>> >>>>>> updateObject(ABeset_gcrma) >>>>>> >>>>>> failing that, you can try something like >>>>>> write.table(ABeset_gcrma at exprs, >>>>>> file="ABeset_gcrma081028orig.txt",uote = FALSE, sep = "\t", >>>>>> col.names = NA) >>>>>> >>>>>> or something like that. >>>>>> >>>>>>> And I enter >>>>>>>> exprs2excel(ABeset_gcrma, file="ABeset_gcrma081028v2.csv") >>>>>>> And I get >>>>>>> Error: could not find function "exprs2excel" >>>>>> That function has been made defunct. >>>>>>> Am I doing something wrong? >>>>>> No, you just can't expect that things won't change. >>>>>> >>>>>> best wishes >>>>>> Robert >>>>>> >>>>>>> Thank you >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>>> _______________________________________________ >>>>> 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 >>>>> > >> _______________________________________________ >> 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 > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v2.0.9 (GNU/Linux) > Comment: Using GnuPG with SUSE - http://enigmail.mozdev.org > > iEYEARECAAYFAkkHYKAACgkQ6fE3kSKck1NjswCfQmXWj+2ny14EFrCB+4eNinxo > kOkAnRAK5j9/K01A3zHf80OR2akCmL6P > =NtCJ > -----END PGP SIGNATURE-----

Thank you, got it exprs(obj) is missing from the output but shows in ?ExpressionSet and puts up the data so I can see it And now perhaps one final question to understanding this old data and progress Long long ago I did AA_ReadAffy <- ReadAffy() ABeset_gcrma < gcrma (AA_ReadAffy) Now I do AA_ReadAffy081031 <- ReadAffy() #on the same .cel files ABeset_gcrma081031 <- gcrma (AA_ReadAffy081031) Then I do Show(ABeset_gcrma) and exprs(ABeset_gcrma081031) And they do not match, for example Probe set Ssc.10026.1.A1_at ABeset_gcrma is 4.124689 ABeset_gcrma081031 is 3.344443 ReadAffy changed? gcrma changed? > From: Martin Morgan <mtmorgan at="" fhcrc.org=""> > Organization: Fred Hutchinson Cancer Research Center > Date: Fri, 31 Oct 2008 11:08:06 -0700 > To: Loren Engrav <engrav at="" u.washington.edu=""> > Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: Re: [BioC] Does old workspace work? > > Loren Engrav wrote: >> Got it, thank you >> So the new ExpressionSets are Ok, cool >> But one thing as I am still exploring the old data and the new >> If I do show(obj) with the old exprSet I can see the data in the file >> If I do show(obj) with the new ExpressionSet I just get a summary >> How do I show(obj) and see the data in the new ExpressionSet >> I checked ?show and google but could not find the answer > >> library(Biobase) >> data(sample.ExpressionSet) >> obj <- sample.ExpressionSet # easier to type# >> obj > ExpressionSet (storageMode: lockedEnvironment) > assayData: 500 features, 26 samples > element names: exprs, se.exprs > phenoData > sampleNames: A, B, ..., Z (26 total) > varLabels and varMetadata description: > sex: Female/Male > type: Case/Control > score: Testing Score > featureData > featureNames: AFFX-MurIL2_at, AFFX-MurIL10_at, ..., 31739_at (500 total) > fvarLabels and fvarMetadata description: none > experimentData: use 'experimentData(object)' > Annotation: hgu95av2 > > The output is meant to suggest how to access elements, e.g., > >> assayData(obj) > <environment: 0xf00858=""> >> assayData(obj) > <environment: 0xf00858=""> >> sampleNames(obj) > [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" > "Q" "R" "S" > [20] "T" "U" "V" "W" "X" "Y" "Z" >> phenoData(obj) > An object of class "AnnotatedDataFrame" > sampleNames: A, B, ..., Z (26 total) > varLabels and varMetadata description: > sex: Female/Male > type: Case/Control > score: Testing Score > > details are on ?ExpressionSet and related classes. > > Martin > >>> sessionInfo() >> R version 2.8.0 Patched (2008-10-26 r46783) >> i386-apple-darwin9.5.0 >> >> locale: >> C >> >> attached base packages: >> [1] tools stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] Biobase_2.2.0 >> >> >> >>> From: Martin Morgan <mtmorgan at="" fhcrc.org=""> >>> Date: Thu, 30 Oct 2008 15:42:44 -0700 >>> To: Loren Engrav <engrav at="" u.washington.edu=""> >>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >>> Subject: Re: [BioC] Does old workspace work? >>> >>> Loren Engrav wrote: >>>> Thank you >>>> >>>> str(obj) returned >>>> @ se.exprs : num [0 , 0] >>>> so I guess there were none >>>> >>>> I find on the web se.exprs is/was standard error estimates >>>> >>>> The old object came in Jan Feb Mar of 2007 as below >>>> >>>> AA_ReadAffy <- ReadAffy() to read 60 Affy .cel files >>>> ABeset_gcrma <- gcrma (AA_ReadAffy) to gcrma it >>>> >>>> After the above I went on and did library (maanova) stuff >>>> >>>> Does it matter if the old ABeset_gcrma object had no std error estimates? >>> Few downstream steps made use of the standard errors, and many upstream >>> methods (including gcrma) didn't / couldn't produce standard errors. >>> >>> Martin >>> >>>>> From: Martin Morgan <mtmorgan at="" fhcrc.org=""> >>>>> Date: Thu, 30 Oct 2008 13:33:55 -0700 >>>>> To: Loren Engrav <engrav at="" u.washington.edu=""> >>>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >>>>> Subject: Re: [BioC] Does old workspace work? >>>>> >>>>> Hi Loren -- >>>>> >>>>> Loren Engrav <engrav at="" u.washington.edu=""> writes: >>>>> >>>>>> With the show(obj) function and the write.table function, I can see the >>>>>> stuff in the old objects so that may solve the immediate problem >>>>>> >>>>>> But changing exprSet to ExpressionSet is attractive >>>>>> And I see it has been discussed before (see below) >>>>>> >>>>>> =========================== >>>>>> [BioC] Error loading, on Bioconductor 1.8, exprSet generated with >>>>>> bioconductor 1.7 >>>>>> Martin Morgan mtmorgan at fhcrc.org >>>>>> Thu Jun 8 18:11:14 CEST 2006 >>>>>> >>>>>> Previous message: [BioC] Error loading, on Bioconductor 1.8, >>>>>> exprSet generated with bioconductor 1.7 >>>>>> Next message: [BioC] [SPAM] Re: Error loading, on Bioconductor >>>>>> 1.8, >>>>>> exprSet generated with bioconductor 1.7 >>>>>> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] >>>>>> >>>>>> Hi Raf, >>>>>> >>>>>> Thanks for the clarification. It sounds like you've found a good >>>>>> solution. >>>>>> >>>>>> The long-term intention is to move away from exprSet as the basic >>>>>> building block, and toward a similar 'ExpressionSet' class. With this >>>>>> in mind, you could also have done (with the current version of >>>>>> Biobase) >>>>>> >>>>>>> obj <- as(tr7.rma, "ExpressionSet") >>>>>> to obtain an ExpressionSet from your (broken) exprSet. An >>>>>> ExpressionSet has methods like exprs(), phenoData(), and pData() that >>>>>> work as exprSet methods, so for many purposes having an ExpressionSet >>>>>> is a great replacement for exprSet. >>>>>> >>>>>> It's important to be able to return to previous versions of objects, >>>>>> and make them 'current'. To that end, the development version of >>>>>> Biobase introduces ways of 'versioning' objects (so that it's easy to >>>>>> figure out when the object was created) and an 'updateObject' method >>>>>> to bring an object up to date. So in the next release of Biobase >>>>>> (available to those already using the 'development' branch of R) >>>>>> you'll be able to >>>>>> >>>>>>> obj <- updateObject(tr76.rma) >>>>>> and stand a reasonable chance of getting an object that satisfies the >>>>>> current definition of exprSet. >>>>>> ============================================= >>>>>> >>>>>> So I try >>>>>>> ABeset_gcrmaExpressionSet <- as (ABeset_gcrma, "ExpressionSet") >>>>>> And get >>>>>> >>>>>> Loading required package: Biobase >>>>>> Loading required package: tools >>>>>> >>>>>> Welcome to Bioconductor >>>>>> >>>>>> Vignettes contain introductory material. To view, type >>>>>> 'openVignette()'. To cite Bioconductor, see >>>>>> 'citation("Biobase")' and for packages 'citation(pkgname)'. >>>>>> >>>>>> Warning message: >>>>>> In asMethod(object) : >>>>>> missing or mis-shaped 'se.exprs' in original object; creating >>>>>> ExpressionSet without se.exprs >>>>> At this point I think ABeset_gcrmaExpressionSet is fine; this is a >>>>> 'warning' message, not an error. The exprSet instance was 'supposed' >>>>> to contain an se.exprs matrix, but my guess is that ABeset_gcrma did >>>>> not (many exprSet instances did not). You might have luck with >>>>> >>>>>> str(ABeset_gcrma) >>>>> you might see something like (it's a little hard to recreate this on >>>>> 2.8.0) >>>>> >>>>> Formal class 'exprSet' [package "Biobase"] with 8 slots >>>>> ..@ exprs : num [1:500, 1:26] 192.7 97.1 45.8 >>>>> .. ..- attr(*, "dimnames")=List of 2 >>>>> .. .. ..$ : chr [1:500] "AFFX-MurIL2_at" "AFFX-MurIL10_at" >>>>> .. .. ..$ : chr [1:26] "A" "B" "C" "D" ... >>>>> ..@ se.exprs : num [1:500, 1:26] 2.85 3.24 3.05 >>>>> .. ..- attr(*, "dimnames")=List of 2 >>>>> .. .. ..$ : chr [1:500] "AFFX-MurIL2_at" "AFFX-MurIL10_at" >>>>> .. .. ..$ : chr [1:26] "A" "B" "C" "D" ... >>>>> >>>>> etc if se.exprs has dimensions 0 (instead of 'chr [1:500]' and 'chr >>>>> [1:26]' in the example above) then the se.exprs was missing or empty >>>>> and hence its loss not important. If it's not missing, then you can >>>>> decide how aggressively you want to rehabilitate your data. Likely >>>>> you'll be able to retrieve the se.exprs with >>>>> >>>>>> se <- slot(ABeset_gcrma, "se.exprs") >>>>> manipulate it to have the same dimenions and dimnames as your >>>>> ExpressionSet has, and add it, e.g., >>>>> >>>>>> assayData(ABeset_gcrmaExpressionSet)[["se.exprs"]] <- se >>>>> I think normally you'll not have to go through these steps though, the >>>>> se.exprs of exprSet will have had no data in it. >>>>> >>>>>> Then I try >>>>>>> ABeset_gcrmaUPDATE <- updateObject(ABeset_gcrma) >>>>>> And get >>>>>> Error in updateObjectFromSlots(object, ..., verbose = verbose) : >>>>>> could not updateObject to class 'phenoData' >>>>>> consider defining an 'updateObject' method for class 'phenoData' >>>>> updateObject is meant to update 'within a class', e.g., from an old >>>>> version of ExpressionSet to a new version of ExpressionSet. Use 'as' >>>>> and you are probably ok. >>>>> >>>>> There may be issues, especially with very old exprSets, so let me know >>>>> if you have problems. >>>>> >>>>> Martin >>>>> >>>>> >>>>>> All with >>>>>>> sessionInfo() >>>>>> R version 2.8.0 Patched (2008-10-26 r46783) >>>>>> i386-apple-darwin9.5.0 >>>>>> >>>>>> locale: >>>>>> C >>>>>> >>>>>> attached base packages: >>>>>> [1] tools stats graphics grDevices utils datasets methods >>>>>> base >>>>>> >>>>>> other attached packages: >>>>>> [1] Biobase_2.2.0 >>>>>> >>>>>>> .Machine$sizeof.pointer >>>>>> [1] 8 >>>>>> >>>>>> Now since I can "see" the data with show and write.table I should >>>>>> probably >>>>>> quit, but for the fun of it, are either of these messages a "quick fix" >>>>>> for >>>>>> a novice? >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> From: Robert Gentleman <rgentlem at="" fhcrc.org=""> >>>>>>> Date: Tue, 28 Oct 2008 11:57:36 -0700 >>>>>>> To: Loren Engrav <engrav at="" u.washington.edu=""> >>>>>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >>>>>>> Subject: Re: [BioC] Does old workspace work? >>>>>>> >>>>>>> -----BEGIN PGP SIGNED MESSAGE----- >>>>>>> Hash: SHA1 >>>>>>> >>>>>>> Re the quality of the link: You need to ask the owner, not this list >>>>>>> >>>>>>> and the answer to your second question is that it depends on what you >>>>>>> want to catch up on. Ideally packages should have up to date vignettes, >>>>>>> and they are your main starting point. Contact maintainers if the >>>>>>> vignettes are incomplete or out of date. >>>>>>> >>>>>>> best wishes >>>>>>> Robert >>>>>>> >>>>>>> Loren Engrav wrote: >>>>>>>> Ok, I can deal with change >>>>>>>> >>>>>>>> One more question, to learn about and deal with the deprecated stuff >>>>>>>> >>>>>>>> Is the file at the url below current, or out of date? >>>>>>>> >>>>>>>> >>>> http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManua l.html#Bio >>>> >> >>>> C >>>>>>>> primer >>>>>>>> >>>>>>>> If it is out of date, is there a better url to catch up fast? >>>>>>>> >>>>>>>>> From: Robert Gentleman <rgentlem at="" fhcrc.org=""> >>>>>>>>> Date: Tue, 28 Oct 2008 09:56:31 -0700 >>>>>>>>> To: Loren Engrav <engrav at="" u.washington.edu=""> >>>>>>>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >>>>>>>>> Subject: Re: [BioC] Does old workspace work? >>>>>>>>> >>>>>>>> Loren Engrav wrote: >>>>>>>>>>> Ok, I will get my stuff modern >>>>>>>>>>> One more question >>>>>>>>>>> Those old saved workspaces and histories might be 32bit from before >>>>>>>>>>> I >>>>>>>>>>> went >>>>>>>>>>> to 64bit >>>>>>>>>>> If they are 32bit workspaces will they work in 64bit (save for the >>>>>>>>>>> deprecated stuff) >>>>>>>> Currently that is the case. But I am not sure how long it will >>>>>>>> remain >>>>>>>> so, as it means that R cannot be truly 64bit, so likely in the next >>>>>>>> year >>>>>>>> or so some change will be needed. Of course, one will always be able >>>>>>>> to >>>>>>>> read 32 bit workspaces in 64bits, but the converse will not likely hold >>>>>>>> for very much longer >>>>>>>> >>>>>>>> Robert >>>>>>>> >>>>>>>> >>>>>>>>>>>> From: Robert Gentleman <rgentlem at="" fhcrc.org=""> >>>>>>>>>>>> Date: Mon, 27 Oct 2008 22:31:21 -0700 >>>>>>>>>>>> To: Loren Engrav <engrav at="" u.washington.edu=""> >>>>>>>>>>>> Cc: "bioconductor at stat.math.ethz.ch" >>>>>>>>>>>> <bioconductor at="" stat.math.ethz.ch=""> >>>>>>>>>>>> Subject: Re: [BioC] Does old workspace work? >>>>>>>>>>>> >>>>>>>>>>>> Hi, >>>>>>>>>>>> >>>>>>>>>>>> Loren Engrav wrote: >>>>>>>>>>>> sessionInfo() >>>>>>>>>>>> R version 2.8.0 Patched (2008-10-26 r46783) >>>>>>>>>>>> i386-apple-darwin9.5.0 >>>>>>>>>>>> >>>>>>>>>>>> locale: >>>>>>>>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>>>>>>>>>> >>>>>>>>>>>> attached base packages: >>>>>>>>>>>> [1] splines tools stats graphics grDevices utils >>>>>>>>>>>> datasets >>>>>>>>>>>> methods base >>>>>>>>>>>> >>>>>>>>>>>> other attached packages: >>>>>>>>>>>> [1] simpleaffy_2.18.0 genefilter_1.22.0 survival_2.34-1 >>>>>>>>>>>> affyio_1.10.0 >>>>>>>>>>>> porcinecdf_2.3.0 gcrma_2.14.0 matchprobes_1.14.0 >>>>>>>>>>>> affy_1.20.0 >>>>>>>>>>>> Biobase_2.2.0 >>>>>>>>>>>> >>>>>>>>>>>> loaded via a namespace (and not attached): >>>>>>>>>>>> [1] AnnotationDbi_1.4.0 DBI_0.2-4 RSQLite_0.7-1 >>>>>>>>>>>> annotate_1.20.0 preprocessCore_1.4.0 >>>>>>>>>>>> >>>>>>>>>>>> ============== >>>>>>>>>>>> A year or so ago I ran 64bit R on Mac PPC and saved various >>>>>>>>>>>> workspaces >>>>>>>>>>>> >>>>>>>>>>>> Now am running 64bit R on Intel 2x3.2 QuadCore and MacOS 10.5.5 >>>>>>>>>>>> >>>>>>>>>>>> I load up the old workspaces >>>>>>>>>>>> and I enter >>>>>>>>>>>> >>>>>>>>>>>> write.exprs(ABeset_gcrma, file="ABeset_gcrma081028orig.txt") >>>>>>>>>>>> Where ABeset_gcrma is an old file >>>>>>>>>>>> >>>>>>>>>>>> and I get >>>>>>>>>>>> Error in function (classes, fdef, mtable) : >>>>>>>>>>>> unable to find an inherited method for function "write.exprs", for >>>>>>>>>>>> signature >>>>>>>>>>>> "exprSet" >>>>>>>>>>>> >>>>>>>>>>>> It was probably more than a year ago - the exprSet class was >>>>>>>>>>>> deprecated and subsequently made defunct. >>>>>>>>>>>> >>>>>>>>>>>> You could try to do: >>>>>>>>>>>> library(Biobase) >>>>>>>>>>>> >>>>>>>>>>>> updateObject(ABeset_gcrma) >>>>>>>>>>>> >>>>>>>>>>>> failing that, you can try something like >>>>>>>>>>>> write.table(ABeset_gcrma at exprs, >>>>>>>>>>>> file="ABeset_gcrma081028orig.txt",uote = FALSE, sep = "\t", >>>>>>>>>>>> col.names = NA) >>>>>>>>>>>> >>>>>>>>>>>> or something like that. >>>>>>>>>>>> >>>>>>>>>>>> And I enter >>>>>>>>>>>> exprs2excel(ABeset_gcrma, file="ABeset_gcrma081028v2.csv") >>>>>>>>>>>> And I get >>>>>>>>>>>> Error: could not find function "exprs2excel" >>>>>>>>>>>> That function has been made defunct. >>>>>>>>>>>> Am I doing something wrong? >>>>>>>>>>>> No, you just can't expect that things won't change. >>>>>>>>>>>> >>>>>>>>>>>> best wishes >>>>>>>>>>>> Robert >>>>>>>>>>>> >>>>>>>>>>>> Thank you >>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> 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 >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> 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 >>>>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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 >>>>>>> -----BEGIN PGP SIGNATURE----- >>>>>>> Version: GnuPG v2.0.9 (GNU/Linux) >>>>>>> Comment: Using GnuPG with SUSE - http://enigmail.mozdev.org >>>>>>> >>>>>>> iEYEARECAAYFAkkHYKAACgkQ6fE3kSKck1NjswCfQmXWj+2ny14EFrCB+4eNinxo >>>>>>> kOkAnRAK5j9/K01A3zHf80OR2akCmL6P >>>>>>> =NtCJ >>>>>>> -----END PGP SIGNATURE----- >>>>>> _______________________________________________ >>>>>> 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 >>>> _______________________________________________ >>>> 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 >> >> _______________________________________________ >> 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

Actually exprs(obj) does show, indented, sorry Thank you, got it exprs(obj) is missing from the output but shows in ?ExpressionSet and puts up the data so I can see it And now perhaps one final question to understanding this old data and progress Long long ago I did AA_ReadAffy <- ReadAffy() ABeset_gcrma < gcrma (AA_ReadAffy) Now I do AA_ReadAffy081031 <- ReadAffy() #on the same .cel files ABeset_gcrma081031 <- gcrma (AA_ReadAffy081031) Then I do Show(ABeset_gcrma) and exprs(ABeset_gcrma081031) And they do not match, for example Probe set Ssc.10026.1.A1_at ABeset_gcrma is 4.124689 ABeset_gcrma081031 is 3.344443 ReadAffy changed? gcrma changed? > From: Martin Morgan <mtmorgan at="" fhcrc.org=""> > Organization: Fred Hutchinson Cancer Research Center > Date: Fri, 31 Oct 2008 11:08:06 -0700 > To: Loren Engrav <engrav at="" u.washington.edu=""> > Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: Re: [BioC] Does old workspace work? > > Loren Engrav wrote: >> Got it, thank you >> So the new ExpressionSets are Ok, cool >> But one thing as I am still exploring the old data and the new >> If I do show(obj) with the old exprSet I can see the data in the file >> If I do show(obj) with the new ExpressionSet I just get a summary >> How do I show(obj) and see the data in the new ExpressionSet >> I checked ?show and google but could not find the answer > >> library(Biobase) >> data(sample.ExpressionSet) >> obj <- sample.ExpressionSet # easier to type# >> obj > ExpressionSet (storageMode: lockedEnvironment) > assayData: 500 features, 26 samples > element names: exprs, se.exprs > phenoData > sampleNames: A, B, ..., Z (26 total) > varLabels and varMetadata description: > sex: Female/Male > type: Case/Control > score: Testing Score > featureData > featureNames: AFFX-MurIL2_at, AFFX-MurIL10_at, ..., 31739_at (500 total) > fvarLabels and fvarMetadata description: none > experimentData: use 'experimentData(object)' > Annotation: hgu95av2 > > The output is meant to suggest how to access elements, e.g., > >> assayData(obj) > <environment: 0xf00858=""> >> assayData(obj) > <environment: 0xf00858=""> >> sampleNames(obj) > [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "J" "K" "L" "M" "N" "O" "P" > "Q" "R" "S" > [20] "T" "U" "V" "W" "X" "Y" "Z" >> phenoData(obj) > An object of class "AnnotatedDataFrame" > sampleNames: A, B, ..., Z (26 total) > varLabels and varMetadata description: > sex: Female/Male > type: Case/Control > score: Testing Score > > details are on ?ExpressionSet and related classes. > > Martin > >>> sessionInfo() >> R version 2.8.0 Patched (2008-10-26 r46783) >> i386-apple-darwin9.5.0 >> >> locale: >> C >> >> attached base packages: >> [1] tools stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] Biobase_2.2.0 >> >> >> >>> From: Martin Morgan <mtmorgan at="" fhcrc.org=""> >>> Date: Thu, 30 Oct 2008 15:42:44 -0700 >>> To: Loren Engrav <engrav at="" u.washington.edu=""> >>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >>> Subject: Re: [BioC] Does old workspace work? >>> >>> Loren Engrav wrote: >>>> Thank you >>>> >>>> str(obj) returned >>>> @ se.exprs : num [0 , 0] >>>> so I guess there were none >>>> >>>> I find on the web se.exprs is/was standard error estimates >>>> >>>> The old object came in Jan Feb Mar of 2007 as below >>>> >>>> AA_ReadAffy <- ReadAffy() to read 60 Affy .cel files >>>> ABeset_gcrma <- gcrma (AA_ReadAffy) to gcrma it >>>> >>>> After the above I went on and did library (maanova) stuff >>>> >>>> Does it matter if the old ABeset_gcrma object had no std error estimates? >>> Few downstream steps made use of the standard errors, and many upstream >>> methods (including gcrma) didn't / couldn't produce standard errors. >>> >>> Martin >>> >>>>> From: Martin Morgan <mtmorgan at="" fhcrc.org=""> >>>>> Date: Thu, 30 Oct 2008 13:33:55 -0700 >>>>> To: Loren Engrav <engrav at="" u.washington.edu=""> >>>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >>>>> Subject: Re: [BioC] Does old workspace work? >>>>> >>>>> Hi Loren -- >>>>> >>>>> Loren Engrav <engrav at="" u.washington.edu=""> writes: >>>>> >>>>>> With the show(obj) function and the write.table function, I can see the >>>>>> stuff in the old objects so that may solve the immediate problem >>>>>> >>>>>> But changing exprSet to ExpressionSet is attractive >>>>>> And I see it has been discussed before (see below) >>>>>> >>>>>> =========================== >>>>>> [BioC] Error loading, on Bioconductor 1.8, exprSet generated with >>>>>> bioconductor 1.7 >>>>>> Martin Morgan mtmorgan at fhcrc.org >>>>>> Thu Jun 8 18:11:14 CEST 2006 >>>>>> >>>>>> Previous message: [BioC] Error loading, on Bioconductor 1.8, >>>>>> exprSet generated with bioconductor 1.7 >>>>>> Next message: [BioC] [SPAM] Re: Error loading, on Bioconductor >>>>>> 1.8, >>>>>> exprSet generated with bioconductor 1.7 >>>>>> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] >>>>>> >>>>>> Hi Raf, >>>>>> >>>>>> Thanks for the clarification. It sounds like you've found a good >>>>>> solution. >>>>>> >>>>>> The long-term intention is to move away from exprSet as the basic >>>>>> building block, and toward a similar 'ExpressionSet' class. With this >>>>>> in mind, you could also have done (with the current version of >>>>>> Biobase) >>>>>> >>>>>>> obj <- as(tr7.rma, "ExpressionSet") >>>>>> to obtain an ExpressionSet from your (broken) exprSet. An >>>>>> ExpressionSet has methods like exprs(), phenoData(), and pData() that >>>>>> work as exprSet methods, so for many purposes having an ExpressionSet >>>>>> is a great replacement for exprSet. >>>>>> >>>>>> It's important to be able to return to previous versions of objects, >>>>>> and make them 'current'. To that end, the development version of >>>>>> Biobase introduces ways of 'versioning' objects (so that it's easy to >>>>>> figure out when the object was created) and an 'updateObject' method >>>>>> to bring an object up to date. So in the next release of Biobase >>>>>> (available to those already using the 'development' branch of R) >>>>>> you'll be able to >>>>>> >>>>>>> obj <- updateObject(tr76.rma) >>>>>> and stand a reasonable chance of getting an object that satisfies the >>>>>> current definition of exprSet. >>>>>> ============================================= >>>>>> >>>>>> So I try >>>>>>> ABeset_gcrmaExpressionSet <- as (ABeset_gcrma, "ExpressionSet") >>>>>> And get >>>>>> >>>>>> Loading required package: Biobase >>>>>> Loading required package: tools >>>>>> >>>>>> Welcome to Bioconductor >>>>>> >>>>>> Vignettes contain introductory material. To view, type >>>>>> 'openVignette()'. To cite Bioconductor, see >>>>>> 'citation("Biobase")' and for packages 'citation(pkgname)'. >>>>>> >>>>>> Warning message: >>>>>> In asMethod(object) : >>>>>> missing or mis-shaped 'se.exprs' in original object; creating >>>>>> ExpressionSet without se.exprs >>>>> At this point I think ABeset_gcrmaExpressionSet is fine; this is a >>>>> 'warning' message, not an error. The exprSet instance was 'supposed' >>>>> to contain an se.exprs matrix, but my guess is that ABeset_gcrma did >>>>> not (many exprSet instances did not). You might have luck with >>>>> >>>>>> str(ABeset_gcrma) >>>>> you might see something like (it's a little hard to recreate this on >>>>> 2.8.0) >>>>> >>>>> Formal class 'exprSet' [package "Biobase"] with 8 slots >>>>> ..@ exprs : num [1:500, 1:26] 192.7 97.1 45.8 >>>>> .. ..- attr(*, "dimnames")=List of 2 >>>>> .. .. ..$ : chr [1:500] "AFFX-MurIL2_at" "AFFX-MurIL10_at" >>>>> .. .. ..$ : chr [1:26] "A" "B" "C" "D" ... >>>>> ..@ se.exprs : num [1:500, 1:26] 2.85 3.24 3.05 >>>>> .. ..- attr(*, "dimnames")=List of 2 >>>>> .. .. ..$ : chr [1:500] "AFFX-MurIL2_at" "AFFX-MurIL10_at" >>>>> .. .. ..$ : chr [1:26] "A" "B" "C" "D" ... >>>>> >>>>> etc if se.exprs has dimensions 0 (instead of 'chr [1:500]' and 'chr >>>>> [1:26]' in the example above) then the se.exprs was missing or empty >>>>> and hence its loss not important. If it's not missing, then you can >>>>> decide how aggressively you want to rehabilitate your data. Likely >>>>> you'll be able to retrieve the se.exprs with >>>>> >>>>>> se <- slot(ABeset_gcrma, "se.exprs") >>>>> manipulate it to have the same dimenions and dimnames as your >>>>> ExpressionSet has, and add it, e.g., >>>>> >>>>>> assayData(ABeset_gcrmaExpressionSet)[["se.exprs"]] <- se >>>>> I think normally you'll not have to go through these steps though, the >>>>> se.exprs of exprSet will have had no data in it. >>>>> >>>>>> Then I try >>>>>>> ABeset_gcrmaUPDATE <- updateObject(ABeset_gcrma) >>>>>> And get >>>>>> Error in updateObjectFromSlots(object, ..., verbose = verbose) : >>>>>> could not updateObject to class 'phenoData' >>>>>> consider defining an 'updateObject' method for class 'phenoData' >>>>> updateObject is meant to update 'within a class', e.g., from an old >>>>> version of ExpressionSet to a new version of ExpressionSet. Use 'as' >>>>> and you are probably ok. >>>>> >>>>> There may be issues, especially with very old exprSets, so let me know >>>>> if you have problems. >>>>> >>>>> Martin >>>>> >>>>> >>>>>> All with >>>>>>> sessionInfo() >>>>>> R version 2.8.0 Patched (2008-10-26 r46783) >>>>>> i386-apple-darwin9.5.0 >>>>>> >>>>>> locale: >>>>>> C >>>>>> >>>>>> attached base packages: >>>>>> [1] tools stats graphics grDevices utils datasets methods >>>>>> base >>>>>> >>>>>> other attached packages: >>>>>> [1] Biobase_2.2.0 >>>>>> >>>>>>> .Machine$sizeof.pointer >>>>>> [1] 8 >>>>>> >>>>>> Now since I can "see" the data with show and write.table I should >>>>>> probably >>>>>> quit, but for the fun of it, are either of these messages a "quick fix" >>>>>> for >>>>>> a novice? >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> From: Robert Gentleman <rgentlem at="" fhcrc.org=""> >>>>>>> Date: Tue, 28 Oct 2008 11:57:36 -0700 >>>>>>> To: Loren Engrav <engrav at="" u.washington.edu=""> >>>>>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >>>>>>> Subject: Re: [BioC] Does old workspace work? >>>>>>> >>>>>>> -----BEGIN PGP SIGNED MESSAGE----- >>>>>>> Hash: SHA1 >>>>>>> >>>>>>> Re the quality of the link: You need to ask the owner, not this list >>>>>>> >>>>>>> and the answer to your second question is that it depends on what you >>>>>>> want to catch up on. Ideally packages should have up to date vignettes, >>>>>>> and they are your main starting point. Contact maintainers if the >>>>>>> vignettes are incomplete or out of date. >>>>>>> >>>>>>> best wishes >>>>>>> Robert >>>>>>> >>>>>>> Loren Engrav wrote: >>>>>>>> Ok, I can deal with change >>>>>>>> >>>>>>>> One more question, to learn about and deal with the deprecated stuff >>>>>>>> >>>>>>>> Is the file at the url below current, or out of date? >>>>>>>> >>>>>>>> >>>> http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManua l.html#Bio >>>> >> >>>> C >>>>>>>> primer >>>>>>>> >>>>>>>> If it is out of date, is there a better url to catch up fast? >>>>>>>> >>>>>>>>> From: Robert Gentleman <rgentlem at="" fhcrc.org=""> >>>>>>>>> Date: Tue, 28 Oct 2008 09:56:31 -0700 >>>>>>>>> To: Loren Engrav <engrav at="" u.washington.edu=""> >>>>>>>>> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >>>>>>>>> Subject: Re: [BioC] Does old workspace work? >>>>>>>>> >>>>>>>> Loren Engrav wrote: >>>>>>>>>>> Ok, I will get my stuff modern >>>>>>>>>>> One more question >>>>>>>>>>> Those old saved workspaces and histories might be 32bit from before >>>>>>>>>>> I >>>>>>>>>>> went >>>>>>>>>>> to 64bit >>>>>>>>>>> If they are 32bit workspaces will they work in 64bit (save for the >>>>>>>>>>> deprecated stuff) >>>>>>>> Currently that is the case. But I am not sure how long it will >>>>>>>> remain >>>>>>>> so, as it means that R cannot be truly 64bit, so likely in the next >>>>>>>> year >>>>>>>> or so some change will be needed. Of course, one will always be able >>>>>>>> to >>>>>>>> read 32 bit workspaces in 64bits, but the converse will not likely hold >>>>>>>> for very much longer >>>>>>>> >>>>>>>> Robert >>>>>>>> >>>>>>>> >>>>>>>>>>>> From: Robert Gentleman <rgentlem at="" fhcrc.org=""> >>>>>>>>>>>> Date: Mon, 27 Oct 2008 22:31:21 -0700 >>>>>>>>>>>> To: Loren Engrav <engrav at="" u.washington.edu=""> >>>>>>>>>>>> Cc: "bioconductor at stat.math.ethz.ch" >>>>>>>>>>>> <bioconductor at="" stat.math.ethz.ch=""> >>>>>>>>>>>> Subject: Re: [BioC] Does old workspace work? >>>>>>>>>>>> >>>>>>>>>>>> Hi, >>>>>>>>>>>> >>>>>>>>>>>> Loren Engrav wrote: >>>>>>>>>>>> sessionInfo() >>>>>>>>>>>> R version 2.8.0 Patched (2008-10-26 r46783) >>>>>>>>>>>> i386-apple-darwin9.5.0 >>>>>>>>>>>> >>>>>>>>>>>> locale: >>>>>>>>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>>>>>>>>>>> >>>>>>>>>>>> attached base packages: >>>>>>>>>>>> [1] splines tools stats graphics grDevices utils >>>>>>>>>>>> datasets >>>>>>>>>>>> methods base >>>>>>>>>>>> >>>>>>>>>>>> other attached packages: >>>>>>>>>>>> [1] simpleaffy_2.18.0 genefilter_1.22.0 survival_2.34-1 >>>>>>>>>>>> affyio_1.10.0 >>>>>>>>>>>> porcinecdf_2.3.0 gcrma_2.14.0 matchprobes_1.14.0 >>>>>>>>>>>> affy_1.20.0 >>>>>>>>>>>> Biobase_2.2.0 >>>>>>>>>>>> >>>>>>>>>>>> loaded via a namespace (and not attached): >>>>>>>>>>>> [1] AnnotationDbi_1.4.0 DBI_0.2-4 RSQLite_0.7-1 >>>>>>>>>>>> annotate_1.20.0 preprocessCore_1.4.0 >>>>>>>>>>>> >>>>>>>>>>>> ============== >>>>>>>>>>>> A year or so ago I ran 64bit R on Mac PPC and saved various >>>>>>>>>>>> workspaces >>>>>>>>>>>> >>>>>>>>>>>> Now am running 64bit R on Intel 2x3.2 QuadCore and MacOS 10.5.5 >>>>>>>>>>>> >>>>>>>>>>>> I load up the old workspaces >>>>>>>>>>>> and I enter >>>>>>>>>>>> >>>>>>>>>>>> write.exprs(ABeset_gcrma, file="ABeset_gcrma081028orig.txt") >>>>>>>>>>>> Where ABeset_gcrma is an old file >>>>>>>>>>>> >>>>>>>>>>>> and I get >>>>>>>>>>>> Error in function (classes, fdef, mtable) : >>>>>>>>>>>> unable to find an inherited method for function "write.exprs", for >>>>>>>>>>>> signature >>>>>>>>>>>> "exprSet" >>>>>>>>>>>> >>>>>>>>>>>> It was probably more than a year ago - the exprSet class was >>>>>>>>>>>> deprecated and subsequently made defunct. >>>>>>>>>>>> >>>>>>>>>>>> You could try to do: >>>>>>>>>>>> library(Biobase) >>>>>>>>>>>> >>>>>>>>>>>> updateObject(ABeset_gcrma) >>>>>>>>>>>> >>>>>>>>>>>> failing that, you can try something like >>>>>>>>>>>> write.table(ABeset_gcrma at exprs, >>>>>>>>>>>> file="ABeset_gcrma081028orig.txt",uote = FALSE, sep = "\t", >>>>>>>>>>>> col.names = NA) >>>>>>>>>>>> >>>>>>>>>>>> or something like that. >>>>>>>>>>>> >>>>>>>>>>>> And I enter >>>>>>>>>>>> exprs2excel(ABeset_gcrma, file="ABeset_gcrma081028v2.csv") >>>>>>>>>>>> And I get >>>>>>>>>>>> Error: could not find function "exprs2excel" >>>>>>>>>>>> That function has been made defunct. >>>>>>>>>>>> Am I doing something wrong? >>>>>>>>>>>> No, you just can't expect that things won't change. >>>>>>>>>>>> >>>>>>>>>>>> best wishes >>>>>>>>>>>> Robert >>>>>>>>>>>> >>>>>>>>>>>> Thank you >>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> 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 >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> 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 >>>>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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 >>>>>>> -----BEGIN PGP SIGNATURE----- >>>>>>> Version: GnuPG v2.0.9 (GNU/Linux) >>>>>>> Comment: Using GnuPG with SUSE - http://enigmail.mozdev.org >>>>>>> >>>>>>> iEYEARECAAYFAkkHYKAACgkQ6fE3kSKck1NjswCfQmXWj+2ny14EFrCB+4eNinxo >>>>>>> kOkAnRAK5j9/K01A3zHf80OR2akCmL6P >>>>>>> =NtCJ >>>>>>> -----END PGP SIGNATURE----- >>>>>> _______________________________________________ >>>>>> 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 >>>> _______________________________________________ >>>> 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 >> >> _______________________________________________ >> 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