[BioC] help with Starr

[Martin Morgan]

On 05/30/2011 07:10 AM, YBao wrote:
> Dear BioConductors,
>
> While trying to go over the demo data in the package Starr, I
> encountered this error message:
>
>> dataPath<- system.file("extdata", package = "Starr")
>> bpmapChr1<- readBpmap(file.path(dataPath, "Scerevisiae_tlg_chr1.bpmap"))
>> cels<- c(file.path(dataPath, "Rpb3_IP_chr1.cel"), file.path(dataPath, "wt_IP_chr1.cel"), file.path(dataPath, "Rpb3_IP2_chr1.cel"))
>> names<- c("rpb3_1", "wt_1", "rpb3_2")
>> type<- c("IP", "CONTROL", "IP")
>> rpb3Chr1<- readCelFile(bpmapChr1, cels, names, type, featureData = T, log.it = T)
> Error: could not find function "readCelFile"
>
>> sessionInfo()
> R version 2.12.2 (2011-02-25)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets
> methods   base
>
> other attached packages:
>   [1] affxparser_1.22.1  affy_1.28.0        Ringo_1.14.0
> Matrix_0.999375-46 lattice_0.19-13    limma_3.6.9
> RColorBrewer_1.0-2 Biobase_2.10.0
>   [9] R.utils_1.5.7      R.oo_1.7.4         R.methodsS3_1.2.1
>
> loaded via a namespace (and not attached):
>   [1] affyio_1.18.0         annotate_1.28.1       AnnotationDbi_1.12.0
> DBI_0.2-5             genefilter_1.32.0     preprocessCore_1.12.0
> RSQLite_0.9-3
>   [8] splines_2.12.2        survival_2.36-1       tools_2.12.2
> xtable_1.5-6
>
> Any help? Can it be an issue of R version so the Starr should be used
> in in R Devel?

Hi Yongde --

'Starr' is not listed as 'other attached packages' so I think you're 
missing a

   library(Starr)

The usual advice is to use a current R (2.13) and associated 
Bioconductor packages.

Martin

>
> Best,
>
> Yongde
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793