
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@aon.at
> To: zhbluweb@hotmail.com
> CC: bioconductor@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@treenames <- subtrees
> 
> 5. Replace slot "numtrees" with the number of subsamples
>  > sub.rma@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
> >
> > _______________________________________________
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> > Bioconductor@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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