[BioC] subset in XPS

[cstrato]

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
>
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