Entering edit mode
Francesco Mancuso
▴
110
@francesco-mancuso-4483
Last seen 10.0 years ago
Hi all!
I have some problems using SNPchip package.
When i run the following code
> oligoSet <- new("oligoSnpSet", copyNumber=as.matrix(CopyNumber),
call=crlmmCalls, callProbability=crlmmConf,
annotation=annotation(crlmmOut))
> x <- oligoSet[chromosome(oligoSet) %in% as.character(3), c(1,2)]
> plot(x)
I obtain the following error:
Error in plotCytoband(cytoband = cytoband, new = FALSE,
cytoband.ycoords = op$cytoband.ycoords, :
subscript out of bounds
The strange is that if I plot only chromosome 1 (or a set of
chromosome
that start from 1), it works.
I really would appreciate any help!
Best,
Francesco
This is my R session info
R version 2.14.0 (2011-10-31)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
LC_TIME=English_United States.1252
attached base packages:
[1] grDevices datasets splines graphics stats tcltk utils
methods base
other attached packages:
[1] crlmm_1.12.0 SNPchip_1.18.0
VanillaICE_1.16.1 IRanges_1.12.1
pd.mapping250k.sty_1.4.0 RSQLite_0.10.0 DBI_0.2-5
oligo_1.18.0 oligoClasses_1.16.0
[10] Biobase_2.14.0 svSocket_0.9-52 TinnR_1.0.3
R2HTML_2.2 Hmisc_3.9-0 survival_2.36-10
loaded via a namespace (and not attached):
[1] affxparser_1.26.1 affyio_1.22.0 annotate_1.32.0
AnnotationDbi_1.16.0 Biostrings_2.22.0 bit_1.1-7
cluster_1.14.1 ellipse_0.3-5 ff_2.2-3
genefilter_1.36.0
[11] grid_2.14.0 lattice_0.20-1 mvtnorm_0.9-9991
preprocessCore_1.16.0 svMisc_0.9-63 tools_2.14.0
xtable_1.6-0 zlibbioc_1.0.0
--
*Francesco Mattia Mancuso*
Bioinformatician
- Bioinformatics Core Facility
- Proteomics Core Facility
CRG-Centre for Genomic Regulation (Room 439)
C/ Dr. Aiguader, 88 (Edif. PRBB)
08003 Barcelona, Spain
Mail: francesco.mancuso@crg.eu <mailto:francesco.mancuso@crg.eu>
Phone: +34 933160202
http://www.crg.es/bioinformatics_unit
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