[BioC] help with Starr

YBao yb8d at virginia.edu
Mon May 30 16:10:44 CEST 2011


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?

Best,

Yongde



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