Hi
I am trying to replicate the example in the vignette of cghMCR
package.
I am afraid the data is not bundled in the package, I verified that
they do not exist in the ~/lib/R/cghMCR/data directory.
-burak
> arrayFiles <- list.files(system.file("sampleData", package =
"cghMCR"),
+ full.names = TRUE, pattern = "TCGA")
Warning message:
In list.files(system.file("sampleData", package = "cghMCR"),
full.names = TRUE, :
list.files: '' is not a readable directory
> arrayFiles
character(0)
>
>
> system.file("sampleData", package = "cghMCR")
[1] ""
>
> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices datasets utils methods
[8] base
other attached packages:
[1] cghMCR_1.14.0 arrayQuality_1.24.0 RColorBrewer_1.0-2
[4] gridBase_0.4-3 hexbin_1.20.0 lattice_0.17-26
[7] convert_1.22.0 marray_1.24.0 DNAcopy_1.18.0
[10] limma_3.2.1 org.Hs.eg.db_2.3.6 GSEABase_1.8.0
[13] annotate_1.24.0 RMySQL_0.7-4 Biostrings_2.14.8
[16] IRanges_1.4.9 RUnit_0.4.25 GOstats_2.12.0
[19] graph_1.24.2 Category_2.12.0 GO.db_2.3.5
[22] org.Mm.eg.db_2.3.6 RSQLite_0.8-1 DBI_0.2-5
[25] AnnotationDbi_1.8.1 Biobase_2.6.1
loaded via a namespace (and not attached):
[1] genefilter_1.28.2 RBGL_1.22.0 splines_2.10.1
survival_2.35-7
[5] tools_2.10.1 XML_2.6-0 xtable_1.5-6
>
--
Burak Kutlu, PhD.
Research Scientist
Hood Lab
Institute for Systems Biology
Hi Burak --
On 02/21/2010 09:43 PM, Burak Kutlu wrote:
> Hi
> I am trying to replicate the example in the vignette of cghMCR
package.
> I am afraid the data is not bundled in the package, I verified that
> they do not exist in the ~/lib/R/cghMCR/data directory.
> -burak
>
>> arrayFiles <- list.files(system.file("sampleData", package =
"cghMCR"),
> + full.names = TRUE, pattern = "TCGA")
> Warning message:
> In list.files(system.file("sampleData", package = "cghMCR"),
> full.names = TRUE, :
> list.files: '' is not a readable directory
>> arrayFiles
> character(0)
>>
>>
>> system.file("sampleData", package = "cghMCR")
> [1] ""
What does
library(cghMCR)
system.file(package="cghMCR")
say? The files should _not_ be in a directory called 'data', but in a
directory called 'sampleData'. Here's what I see
> list.files(system.file(package="cghMCR"))
[1] "data" "DESCRIPTION" "doc" "help" "html"
[6] "INDEX" "Meta" "NAMESPACE" "R"
"sampleData"
> list.files(system.file("sampleData", package="cghMCR"))
[1] "TCGA-06-0881-01A-02D-0387-02-short.txt"
[2] "TCGA-12-0818-01A-01D-0387-02-short.txt"
[3] "TCGA-12-0827-01A-01D-0387-02-short.txt"
The output of .libPaths() might also be helpful; you did install
cghMCR
with biocLite(), right?
Martin
> sessionInfo()
R version 2.10.1 Patched (2010-02-23 r51168)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] cghMCR_1.4.0 limma_3.2.1 CNTools_1.2.0
genefilter_1.28.2
[5] DNAcopy_1.20.0
loaded via a namespace (and not attached):
[1] annotate_1.24.0 AnnotationDbi_1.8.1 Biobase_2.6.1
[4] DBI_0.2-4 RSQLite_0.7-3 splines_2.10.1
[7] survival_2.35-8 tools_2.10.1 xtable_1.5-6
>>
>> sessionInfo()
> R version 2.10.1 (2009-12-14)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid stats graphics grDevices datasets utils
methods
> [8] base
>
> other attached packages:
> [1] cghMCR_1.14.0 arrayQuality_1.24.0 RColorBrewer_1.0-2
> [4] gridBase_0.4-3 hexbin_1.20.0 lattice_0.17-26
> [7] convert_1.22.0 marray_1.24.0 DNAcopy_1.18.0
> [10] limma_3.2.1 org.Hs.eg.db_2.3.6 GSEABase_1.8.0
> [13] annotate_1.24.0 RMySQL_0.7-4 Biostrings_2.14.8
> [16] IRanges_1.4.9 RUnit_0.4.25 GOstats_2.12.0
> [19] graph_1.24.2 Category_2.12.0 GO.db_2.3.5
> [22] org.Mm.eg.db_2.3.6 RSQLite_0.8-1 DBI_0.2-5
> [25] AnnotationDbi_1.8.1 Biobase_2.6.1
>
> loaded via a namespace (and not attached):
> [1] genefilter_1.28.2 RBGL_1.22.0 splines_2.10.1
survival_2.35-7
> [5] tools_2.10.1 XML_2.6-0 xtable_1.5-6
>>
>
>
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
