[BioC] [SPAM] Re: Error loading, on Bioconductor 1.8, exprSet generated with bioconductor 1.7
rcaloger
raffaele.calogero at unito.it
Fri Jun 9 09:42:45 CEST 2006
Hi Martin,
many thanks for you kind suggestions and informations.
Yours comments come at the right time since I am starting to play around
with the 'ExpressionSet' class to reorganize the structure of the
applera library we have developed.
Best
Raf
Martin Morgan wrote:
>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.
>
>Finally, the following function might work to update exprSet-like (and
>perhaps other) objects to their current version. This might be useful
>until the next release of Bioconductor.
>
>Martin
>
>updateObject <- function(x, xclass=class(x), verbose=FALSE) {
> if (is(x, "environment")) {
> if (verbose)
> message("returning original object of class 'environment'")
> return(x)
> }
> news <- names(getSlots(xclass))
> if (is.null(news)) {
> if (verbose) message("definition of '", xclass, "' has no slots; ",
> "returning original object")
> return(x)
> }
> errf <- function(...)
> function(err) {
> if (verbose)
> message(..., ":\n ", conditionMessage(err),
> "\n trying next method...")
> NULL
> }
> if (verbose) message("updateObject('", xclass, "')")
> olds <- attributes(unclass(x))
> joint <- intersect(names(olds), news)
> olds[joint] <- lapply(olds[joint], updateObject, verbose=verbose)
> res <- NULL
> if (is.null(res))
> res <-
> tryCatch({
> do.call("new", c(xclass, olds[joint]))
> }, error=errf("'new(\"",xclass,"\", ...)' from slots failed"))
> if (is.null(res))
> res <-
> tryCatch({
> obj <- do.call("new", list(xclass))
> for (slt in joint) slot(obj, slt) <- slot(x, slt)
> obj
> }, error=errf("failed to add slots to 'new(\"",xclass,"\", ...)'"))
> if (is.null(res))
> stop("could not updateObject to class '", xclass, "'")
> validObject(res)
> res
>}
>
>
>
>
>rcaloger <raffaele.calogero at unito.it> writes:
>
>
>
>>You are right, I check the object creation, it was July 2005,
>>therefore it was created with the release 1.6 of Bioconductor.
>>This is the output of the class(tr7.rma)
>>[1] "exprSet"
>>attr(,"package")
>>[1] "Biobase"
>>
>>I manage to see the content of the object with show(tr7.rma) also on
>>Bioconductor 1.8.
>>However, the str(tr7.rma) gives the error
>>
>>Error in FUN(X[[6]], ...) : no slot of name "reporterInfo" for this
>>object of class "exprSet"
>>
>>
>>I have then created a new instace of exprSet in the following way:
>>pd.xx<-new("phenoData")
>>pData(pd.xx)<-pData(tr7.rma)
>>xx<-new('exprSet', exprs = exprs(tr7.rma), phenoData=pd.xx)
>>tr7.rma<-xx
>>
>>I had to recreate also the phenoData instance since the varMetadata
>>variable was missed in my phenoData.
>>However, this problem rise the question: is ti reasonable to use
>>exprSet objects as backup?
>>Thanks for your help
>>Raffaele
>>
>> Martin Morgan wrote:
>>
>>
>>
>>>Raf --
>>>
>>>Can you provide just a bit more information? What's the result of
>>>
>>>
>>>
>>>
>>>
>>>>class(tr7.rma)
>>>>
>>>>
>>>>
>>>>
>>>Also, I suspect that tr7.rma was created not in the last release of
>>>Biobase, but the release before that (at least). I say this because
>>>the 'reporterInfo' slot was present in the 1.7 release.
>>>
>>>In the mean time, I suspect that
>>>
>>>
>>>
>>>
>>>
>>>>show(tr7.rma)
>>>>
>>>>
>>>>
>>>>
>>>will display the contents of your object.
>>>
>>>Martin
>>>
>>>rcaloger <raffaele.calogero at unito.it> writes:
>>>
>>>
>>>
>>>
>>>
>>>>Hi,
>>>>today I was working on an Affy exprSet I saved before the new
>>>>release of Bioconductor (1.8).
>>>>I loaded it but I got the following error when I tried to show it:
>>>>library(affy)
>>>>load("tr7.rma.rda")
>>>>tr7.rma
>>>>Error in slot(object, what) : no slot of name "pubMedIds" for this
>>>>object of class "MIAME"
>>>>
>>>>Furthermore, if I issue the command:
>>>>str(tr7.rma)
>>>>I got this error:
>>>>Error in FUN(X[[6]], ...) : no slot of name "reporterInfo" for this
>>>>object of class "exprSet"
>>>>
>>>>I was expecting that there should be some sort of back
>>>>compatibility with at least the previous release of the exprSet.
>>>>The error comes using the Biobase Version: 1.10.0.
>>>>There is any way to fix the problem or Do I have to install again
>>>>the old release of Bioconductor?
>>>>Thanks
>>>>Raf
>>>>
>>>>
>>>>--
>>>>
>>>>----------------------------------------
>>>>Prof. Raffaele A. Calogero
>>>>Bioinformatics and Genomics Unit
>>>>Dipartimento di Scienze Cliniche e Biologiche
>>>>c/o Az. Ospedaliera S. Luigi
>>>>Regione Gonzole 10, Orbassano
>>>>10043 Torino
>>>>tel. ++39 0116705420
>>>>Lab. ++39 0116705408
>>>>Fax ++39 0119038639
>>>>Mobile ++39 3333827080
>>>>email: raffaele.calogero at unito.it
>>>>www: www.bioinformatica.unito.it
>>>>
>>>>_______________________________________________
>>>>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
>>>>
>>>>
>>>>
>>>>
>>--
>>
>>----------------------------------------
>>Prof. Raffaele A. Calogero
>>Bioinformatics and Genomics Unit
>>Dipartimento di Scienze Cliniche e Biologiche
>>c/o Az. Ospedaliera S. Luigi
>>Regione Gonzole 10, Orbassano
>>10043 Torino
>>tel. ++39 0116705420
>>Lab. ++39 0116705408
>>Fax ++39 0119038639
>>Mobile ++39 3333827080
>>email: raffaele.calogero at unito.it
>>www: www.bioinformatica.unito.it
>>
>>
--
----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
tel. ++39 0116705420
Lab. ++39 0116705408
Fax ++39 0119038639
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
www: www.bioinformatica.unito.it
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