[BioC] LocusLink query problem / bioC basic tutorial

[Robert Gentleman]

Hi,
 You didn't say where you got the tutorial from -- some are very old
 (and I believe that this is one of those ones).

 read.annotation went away about a year ago....

If you are looking at somthing like this
###################################################
### chunk number 14: R
###################################################
ll <- read.annotation("hgu68ll") # Read in locus link annotation data
gname <- row.names(X2)           # Names of genes with small p--value
LocusID<-multiget(gname, env=ll) # Locus link IDs
locuslinkByID(LocusID)		  # Query LocusLink


Then, using the new system (and you probably want to use R 1.7.0
patched rather than 1.6.2). First obtain the hu6800 library

 library(hu6800)
 gname <- row.names(X2)
 LocusID<- getLL(gname, "hu6800")

Robert


On Thu, May 22, 2003 at 08:29:02AM -0400, Huang, Cheng-Cheng (NIH/NCI) wrote:
> All:
> 
> I have a LocusLink query problem when I run Dudoit's "Bioconductor basic
> tutorial".
> > library(annotate)
> > library(genefilter)
> > library(golubEsets)
> > library(ctest)
> > library(MASS)
> > library(mva)
> > library(cluster)
> > read.annotation("hgu6811")
> Error: couldn't find function "read.annotation"
> 
> 
> I am running R1.6.2 on Win2k, All latestest packages are used. According to
> the "help", it seems this function belongs to "annotate" package, which was
> loaded before the function called. Am I missing any packages or data files
> for this chip (hgu6811")?
> 
> Thanks
> 
> cc;
> 
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> Bioconductor at stat.math.ethz.ch
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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
| Department of Biostatistics      office: M1B20                            |
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