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 > > > > > > > > > > > > > -------------------------------------------------------------------- ----