[BioC] se.exprs in Affy
Mary Putt
mputt at cceb.upenn.edu
Tue Jun 24 18:07:22 MEST 2003
I am curious about how to use se.exprs (R version 1.70, . My
understanding is that it can be used with an exprSet to access the
model-based standard errors. In particular the code I have used is:
#rma.ctl is an exprSet generated by normalizing an AffyBatch object
("control") with rma. My understanding is that this object contains
model-based #expression values for each gene and each subject on the
chip
>rma.ctl<-rma(control)
>rma.ctl
Expression Set (exprSet) with
22283 genes
8 samples
phenoData object with 1 variables and 8 cases
varLabels
batch: batch
> exprs.rma<-exprs(rma.ctl)
> dim(exprs.rma)
[1] 22283 8
> exprs.rma[1,]
C:\\cappola/C1.CEL C:\\cappola/C2.CEL C:\\cappola/C3.CEL
C:\\cappola/C4.CEL
6.231048 6.372506 6.115754
6.147328
C:\\cappola/R1.CEL C:\\cappola/R2.CEL C:\\cappola/R3.CEL
C:\\cappola/R4.CEL
6.352380 6.283031 6.426585
6.207264
> se.exprs.rma<-se.exprs(rma.ctl)
> dim(se.exprs)
[1] 22283 8
> se.exprs.rma[1,]
[1] NA NA NA NA NA NA NA NA
I don't understand why the se.exprs.rma matrix is empty? Thanks in
advance, Mary Putt
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