[BioC] subset in XPS

[cstrato]

Dear Zhibin

Meanwhile, I have uploaded a new version to BioC devel:
http://bioconductor.org/packages/2.3/bioc/html/xps.html
which simplifies your request as follows:

1. get expression values
 > value <- exprs(data.rma)
2. select treenames of choice (no extension necessary)
 > treenames <- c("TestA2", "TestB1")
3. make a copy of your object if you do not want to replace it
 > sub.rma <- data.rma
4. replace slot data with subset
exprs(sub.rma, treenames) <- value
5. check if the new ExprTreeSet is correct: 
 > str(sub.rma)

Best regards
Christian


Zhibin Lu wrote:
> Dear Christian,
>
> Thanks so much for such a detailed explanation. I will try this when I 
> get to work next week, and I do not see why I can not follow the 
> direction.
>
> Thanks again and have a nice weekend,
>
> Zhibin
>
> > Date: Sat, 28 Jun 2008 15:46:26 +0200
> > From: cstrato at aon.at
> > To: zhbluweb at hotmail.com
> > CC: bioconductor at stat.math.ethz.ch
> > Subject: Re: [BioC] subset in XPS
> >
> > Dear Zhibin
> >
> > Since you have already done RMA you have now an ExprTreeSet,
> > called e.g. "data.rma". You can see the structure with:
> > > str(data.rma)
> >
> > Since currently there is no direct possibility to use a
> > subset of type ExprTreeSet only, you can create a new class
> > ExprTreeSet in the following way:
> >
> > 1. Make a subset of slot "data" which is a dataframe
> > (assuming that you want to use samples 1,2,3,7,8,9):
> > > subdata <- exprs(data.rma)
> > > subdata <- subdata[,c(1:2,3:5, 9:11)]
> > Please note that it is important to keep the first
> > two columns.
> >
> > 2. Create a copy "sub.rma" of class "data.rma"
> > > sub.rma <- data.rma
> >
> > 3. Replace slot "data" with "subdata":
> > > exprs(sub.rma) <- subdata
> >
> > For the moment you need to replace slots "treenames" and
> > "numtrees", too, which I will change in the future to be
> > done automatically.
> >
> > 4. Replace slot "treenames" with the names of your subset:
> > a, create list containing the sub samples
> > > subtrees <- unlist(treeNames(data.g.rma))
> > > subtrees <- as.list(subtrees[c(1:3,7:9)])
> > b, check if the names are correct:
> > > subtrees
> > c, replace slot "treenames":
> > > sub.rma at treenames <- subtrees
> >
> > 5. Replace slot "numtrees" with the number of subsamples
> > > sub.rma at numtrees <- length(subtrees)
> >
> > 6. Check if the new ExprTreeSet is correct:
> > > str(sub.rma)
> >
> > Now you can use the new ExprTreeSet "sub.rma" as input for
> > method unifilter:
> > > rma.ufr <- unifilter(sub.rma, .......)
> >
> >
> > If you want to take advantage of the advanced capabilties
> > of package "limma", then you can create a Biobase class
> > "ExpressionSet" containing only your 6 samples as described
> > in Appendix A.3 of the vignette xps.pdf:
> >
> > 1. extract the normalized expression data:
> > > subdata <- validData(data.rma)
> >
> > 2. Since "subdata" is a dataframe, simply create a subframe:
> > > subdata <- subdata[,c(1:3,7:9)]
> >
> > 3. Create a Biobase class "ExpressionSet", called "subset"
> > > subset <- new("ExpressionSet", exprs = as.matrix(subdata))
> >
> > Now you have an ExpressionSet ready for use with "limma".
> >
> > Please let me know if you succeeded with this info.
> >
> > Best regards
> > Christian
> > _._._._._._._._._._._._._._._._
> > C.h.i.s.t.i.a.n S.t.r.a.t.o.w.a
> > V.i.e.n.n.a A.u.s.t.r.i.a
> > e.m.a.i.l: cstrato at aon.at
> > _._._._._._._._._._._._._._._._
> >
> > Zhibin Lu wrote:
> > > Hi,
> > >
> > > I am new in R/bioconductor. I am using xps package to analyze 
> Affymetrix Gene ST 1.0 data. After I loaded CEL files into the 
> DataTreeSet and compute the expression level with RMA, can I work on a 
> subset of the data? Say, I have 12 samples. After RMA, can I just work 
> on 6 of them and divide them into two groups and apply UniFilter to 
> just these 6 ones?
> > >
> > > Thanks,
> > >
> > > Zhibin
> > >
> > > _______________________________________________
> > > 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
> > >
> > >
> > >
> >
>
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