[BioC] Labels in exprs to plot

[Adaikalavan Ramasamy]

I would like to contribute this little function if anyone is interested.

exprSet.sampleNames.cleanup <- function(object){
   stopifnot( is(object, "exprSet") )

   cn <- sampleNames(object)
   cn <- sapply( strsplit(cn, split="\/"), function(x) x[ length(x) ] )
   cn <- sub( ".cel$|.CEL$", "", cn)
   sampleNames(object) <- cn
   return(object)
}


On a particular dataset I have, I have the following :

> sampleNames(obj)  # before cleanup

 [1] "/home/adai/tmp/0029_1209_H95Av2_KF0077.cel"
 [2] "/home/adai/tmp/0029_1210_H95A2_KF0079.cel"
 [3] "/home/adai/tmp/0029_1213_H95A2_KF0110.cel"
 [4] "/home/adai/tmp/0029_1221_H95A2_KF0144.cel"
 [5] "/home/adai/tmp/0029_1222_H95A2_KF0146.cel"
 [6] "/home/adai/tmp/0029_1224_HU95A_KF0150.cel"
 [7] "/home/adai/tmp/0029_1225_H95A2_KF0157.CEL"
 [8] "/home/adai/tmp/0029_1237_H95A2_KF0125.CEL"
 [9] "/home/adai/tmp/0029_1238_H95A2_KF0128.CEL"
[10] "/home/adai/tmp/0029_1239_H95A2_KF0131.CEL"
[11] "/home/adai/tmp/0029_1240_H95A2_KF0133.CEL"
[12] "/home/adai/tmp/0029_1377_H95A2_KF-104.CEL"

obj <- exprSet.sampleNames.cleanup(obj)
> sampleNames(obj)  # after cleanup

 [1] "0029_1209_H95Av2_KF0077" "0029_1210_H95A2_KF0079"
 [3] "0029_1213_H95A2_KF0110"  "0029_1221_H95A2_KF0144"
 [5] "0029_1222_H95A2_KF0146"  "0029_1224_HU95A_KF0150"
 [7] "0029_1225_H95A2_KF0157"  "0029_1237_H95A2_KF0125"
 [9] "0029_1238_H95A2_KF0128"  "0029_1239_H95A2_KF0131"
[11] "0029_1240_H95A2_KF0133"  "0029_1377_H95A2_KF-104"



On Sat, 2004-08-14 at 22:11, James MacDonald wrote:
> The easiest way I know to do this is to use list.celfiles() when you
> read in your AffyBatch.
> 
> abatch <- read.affybatch(filenames=list.celfiles())
> 
> If you simply use ReadAffy(), you will get the entire path and will have
> to use sub() to truncate later.
> 
> HTH,
> 
> Jim
> 
> 
> 
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> >>> <mcolosim at brandeis.edu> 08/14/04 10:11 AM >>>
> Hi,
> 
> I'm having the hardest time trying to get the correct labels from my
> exprs to
> plot correctly. I'm using the affy to read in cels and process them.
> However,
> the lables I get are the "fullpath" to the files and not the ones in
> pData.
> 
> Is there a way to get the correct labels minus the .CEL from pData to be
> used
> as labels for plot (even exprs2excel is now printing out the full paths,
> which it didn't do before).
> 
> Basically I clustered my arrays and want to view it, but with the full
> path as
> labels it is tiny.
> 
> hcRMA <- hclust(....)
> plot(hcRMA, labels = ?, main = "Hierarchical clustering dendrogram"
> 
> Thanks
> Marc
> 
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