[Bioc-devel] annaffy/saveHTML problem

[Li, Xuejun]

Hello everyone,

Can anyone help me to solve this problem?

I have been using the saveHTML function (from annaffy) in R-2.5.1, and
it worked fine.  However, this function doesn't work properly under the
R 2.6.0 Pre-release.  For example, if I type the following code under
the R-2.5.1:

library(annaffy)
probeid<-c("1415779_s_at", "1415943_at", "1415944_at")
anncols <- aaf.handler()[c(1,2,8)]
anntable <- aafTableAnn(probeid, "mouse430a2", anncols)
saveHTML(anntable, "example.html", title = "Simple Example")


Under R-2.5.1, the code above will create a table in HTML like the one
below:  

Probe 	 	Symbol 	LocusLink 
1415779_s_at 	Actg1 	11465 
1415943_at 		Sdc1 		20969 
1415944_at 		Sdc1 		20969

However, under R 2.6.0 Pre-release, it will create the following table:

Probe 		Symbol 			LocusLink 
1415779_s_at 	Actg1, Sdc1, Sdc1 	11465, 20969, 20969 
1415943_at 		Actg1, Sdc1, Sdc1 	11465, 20969, 20969 
1415944_at 		Actg1, Sdc1, Sdc1 	11465, 20969, 20969

It seems like the Symbol and LocusLink doesn't merge correctly to Probe.
I wonder how I can change my parameters in saveHTML function in order to
create a correct table.  Thanks!!!



Arthur Xuejun Li
Dept of Biostatistics
City Of Hope
1500 E. Duarte Rd., Duarte CA 91010
Ph.: (626)256-4673 ext.65121



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