[BioC] exonmap, xmap and xmapbridge

Crispin Miller CMiller at picr.man.ac.uk
Wed Feb 6 12:41:53 CET 2008

Hi Paul,

I think you're confusing two functions:

Have a look at the man page for xmapGene()... It (and the related functions
xmapTranscript(), xmapExon() and xmaProbeset()) simply opens up a browser
window on xmap, located at the gene, (or transcript, etc...) specified.

It doesn't do anything with the expression data and simply takes one
parameter, the gene id. The error you're getting is R complaining that
you're calling xmapGene with lots of unused arguments (including eset).

The function xmapBridge() is what you want to use to write out expression
data for the XMapBridge.

It doesn't expect the parameter 'use.bridge', though...

This should work, however!:

xmapBridge(<my gene id>,eset=affy.


On 5/2/08 18:01, "Vincent Carey 525-2265" <stvjc at channing.harvard.edu>

>> 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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