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

[Daniel Brewer]

expr.matrix is a matrix and it did work when I inverted the syntax.

Many thanks

Daniel

Martin Morgan wrote:
> 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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