[BioC] exonmap, xmap and xmapbridge

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Tue Feb 5 19:01:09 CET 2008

> dear all,
> I am trying to plot different gene/transcript/exon expressions from exon
> affymetrix chips by using the function 'xmapGene' or 'xmapBridge'
> (package exonmap). but when I start these functions I get an error
> message, that I have to use <S4 object of class "ExpressionSet"> for
> value 'eset'. I used this code:
>  > raw.data = read.exon()
>  > raw.data at cdfName = "exon.pmcdf"
>  > affy.rma = rma(raw.data)
> Background correcting
> Normalizing
> Calculating Expression
>  > xmapDatabase("Human")
> done.
>  > xmapGene("ENSG00000128655", *eset=affy.rma*,
> use.bridge=TRUE,gps=list(A=1:3,B=4:6),type="fc",overwrite=FALSE)
> Error in xmapGene("ENSG00000128655", *eset = affy.rma*, use.bridge =
> TRUE,  :
>   unused argument(s) (*eset = <S4 object of class "ExpressionSet">*,
> use.bridge = TRUE, gps = list(A = 1:3, B = 4:8), type = "fc", overwrite
> = FALSE)
> I thought that the function rma() results in an S4 object of the class
> "exprSet", isn't it??? and is "exprSet"the same like "ExpressionSet"?
> Is there any chance to get an S4 object of class "ExpressionSet???

Please provide a sessionInfo() result to tell us the versions
of R and the various packages you are using.

"exprSet" is the name of a legacy class that is not to be used in
current applications.  There may be software on your system that
generates "exprSet" instances but it should be updated.

"ExpressionSet" is the name of the class that replaces "exprSet".

In the current version of exonmap, xmapGene has a single parameter "x".
So your call with numerous parameters shown above (hard to decipher)
may not be valid.

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