[BioC] Renaming row names (U133A/B joining problem)

[Martin Morgan]

Hi Daniel,

I think the basic syntax is inverted --

rownames(obj)[1:3] <- 3:1

instead of

rownames(obj[1:3,]) <- 3:1

It's a little hard to tell what expr.matrix is. A matrix?

> m <- matrix(0,10,5)
> rownames(m)[1:4] <- 4:1 # need to have dims before they can be changed!
Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
> rownames(m) <- 1:10
> rownames(m)[1:4] <- 4:1
> m
   [,1] [,2] [,3] [,4] [,5]
4     0    0    0    0    0
3     0    0    0    0    0
2     0    0    0    0    0
1     0    0    0    0    0
5     0    0    0    0    0
6     0    0    0    0    0
7     0    0    0    0    0
8     0    0    0    0    0
9     0    0    0    0    0
10    0    0    0    0    0


But maybe it's an 'ExpressionSet' or 'exprSet'. What does

> class(expr.matrix)

say? If it's an ExpressionSet (or I think also an exprSet), then
you'll want to do the equivalent of

> obj <- new("ExpressionSet", exprs=matrix(0,10,5))
> obj
ExpressionSet (storageMode: lockedEnvironment)
assayData: 10 features, 5 samples 
  element names: exprs 
phenoData
  sampleNames: 1, 2, ..., 5 (5 total)
  varLabels and varMetadata: none
featureData
  featureNames: 1, 2, ..., 10 (10 total)
  varLabels and varMetadata: none
experimentData: use 'experimentData(object)'
Annotation character(0)
> featureNames(obj)
 [1] "1"  "2"  "3"  "4"  "5"  "6"  "7"  "8"  "9"  "10"
> featureNames(obj)[2:4] <- 4:2
> featureNames(obj)
 [1] "1"  "4"  "3"  "2"  "5"  "6"  "7"  "8"  "9"  "10"
> obj
ExpressionSet (storageMode: lockedEnvironment)
assayData: 10 features, 5 samples 
  element names: exprs 
phenoData
  sampleNames: 1, 2, ..., 5 (5 total)
  varLabels and varMetadata: none
featureData
  featureNames: 1, 4, ..., 10 (10 total)
  varLabels and varMetadata: none
experimentData: use 'experimentData(object)'
Annotation character(0)

Hope that helps,

Martin


Daniel Brewer <daniel.brewer at icr.ac.uk> writes:

> Hi,
>
> I have a expression dataset where I want to join Affymetrix U133A and B
> arrays.  The rownames of the expression matrix are set to the probe
> names.  To do this I want to treat all the probe names that are shared
> between the arrays as unique by appending an "_A" or "_B".  I do this by
> finding the names of the probe that are shared and then running:
>
> rownames(expr.matrix[match(ProbeIntersect,rownames(expr.matrix)),]) <-
> paste(rownames(expr.matrix[match(ProbeIntersect,rownames(expr.matrix)),]),"_A",sep="")
>
> Where "expr.matrix" is the expression matrix and "ProbeIntersect" is the
> list of probe names that are shared.  This command though does not seem
> to change the row names.  Any idea what I am doing wrong?
>
> Thanks
>
> Daniel
>
> -- 
> **************************************************************
>
> Daniel Brewer, Ph.D.
> Institute of Cancer Research
> Email: daniel.brewer at icr.ac.uk
>
> **************************************************************
>
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.
>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org