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Dear All,
I am working on Agilent 244k aCGH files and am ultimately segmenting
them with DNAcopy.
I have succeeded in doing this by creating the CNA files that
DNAcopy???s smooth.CNA function needs but I wonder if this is the
right strategy as I required the readPositionalInfo function from
another package, snapCGH, to create those files and encountered some
problems.
I needed readPositionalInfo to create Chr and Position fields for the
CNA object but the function errored and needed fixing.
The first problem was that readPositionalInfo contains this line at
the end of a switch section :
???stop("Source argument not recognised"), )???
The comma (penultimate character) seems to tell R that there are two
defaults and results in the error "duplicate switch defaults:
'stop("Sour...' and ''"
This seems to have been reported elsewhere:
http://grokbase.com/t/r/bioconductor/128r956jfk/bioc-
readpositionalinfo
Another issue seems to be that readPositionalInfo doesn't actually
create a variable called Position (of gene - it creates variables
called start and end instead) which creates problems when subsequently
using the MAList object in processCGH or to create a CNA object for
segmenting in DNAcopy. This has been found before
https://stat.ethz.ch/pipermail/bioconductor/2009-September/029519.html
I fixed this as other have done by creating position to be
(start+end)/2.
I wondered if the steps I have used are correct and standard as I am
surprised that a commonly used function would apparently have errors
or require work-arounds. Or maybe I am using it incorrectly.
Many thanks in advance for any specific or general advice on my
analysis
Bernard North
-- output of sessionInfo():
R version 3.0.0 (2013-04-03)
Platform: i386-w64-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] snapCGH_1.30.0 DNAcopy_1.34.0 limma_3.16.5
[4] BiocInstaller_1.10.2
loaded via a namespace (and not attached):
[1] aCGH_1.38.0 affy_1.38.1 affyio_1.28.0
[4] annotate_1.38.0 AnnotationDbi_1.22.6 Biobase_2.20.1
[7] BiocGenerics_0.6.0 cluster_1.14.4 DBI_0.2-7
[10] genefilter_1.42.0 GLAD_2.24.0 grid_3.0.0
[13] IRanges_1.18.1 lattice_0.20-15 MASS_7.3-27
[16] multtest_2.16.0 parallel_3.0.0 pixmap_0.4-11
[19] preprocessCore_1.22.0 RColorBrewer_1.0-5 RSQLite_0.11.4
[22] splines_3.0.0 stats4_3.0.0 strucchange_1.4-7
[25] survival_2.37-4 tilingArray_1.38.0 tools_3.0.0
[28] vsn_3.28.0 XML_3.98-1.1 xtable_1.7-1
[31] zlibbioc_1.6.0
--
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