[BioC] exprSet in alongChrom from geneplotter

[Heidi Dvinge]

Hi all

I'm playing around with a couple of different chromosome plots. Among
others, I'm trying to use the function alongChrom from geneplotter pkg,
but it seems like it hasn't really been updated from exprSet to
ExpressionSet yet, although I'm using the latest version (sessionInfo
below).

Example:

> data(ALL)
> z <- buildChromLocation("hgu95av2")
> alongChrom(ALL, "X", z)
Error in getACExprs(eSet, usedGenes, plotFormat, scale) :
  no slot of name "exprs" for this object of class "ExpressionSet"
In addition: Warning message:
'geneNames' is deprecated.
Use 'featureNames' instead.
See help("Deprecated")

If I look at geneplotter:::getACExprs it seems to point back to the line
that says
>    chromExprs <- eSet at exprs[names(usedGenes), ]
instead of
>     chromExprs <- exprs(eSet)[names(usedGenes), ]

Has the use of the alongChrom function generally been replaced by
something else?

Thanks
\Heidi

> sessionInfo()
R version 2.6.0 Under development (unstable) (2007-07-17 r42258)
i386-apple-darwin8.10.1

locale:
en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets 
methods   base

other attached packages:
 [1] ALL_1.4.3             PFAM_1.17.0           Category_2.3.14      
GO_1.17.0
 [5] KEGG_1.17.0           graph_1.15.7          mouse4302_1.17.0     
mouse430a2_1.17.0
 [9] hgu95av2_1.17.0       genefilter_1.15.3     survival_2.32        
geneplotter_1.15.1
[13] lattice_0.16-1        annotate_1.15.2       AnnotationDbi_0.0.78 
RSQLite_0.6-2
[17] DBI_0.2-3             gcrma_2.9.1           matchprobes_1.9.8    
limma_2.11.6
[21] affy_1.15.7           preprocessCore_0.99.7 affyio_1.5.4         
Biobase_1.15.14

loaded via a namespace (and not attached):
[1] KernSmooth_2.22-20 RBGL_1.13.3        RColorBrewer_1.0-1
cluster_1.11.7     grid_2.6.0