Entering edit mode
Michael MOZAR
▴
60
@michael-mozar-4289
Last seen 9.6 years ago
hello, i've got a problem when i want ti create a package to use with
the
oligo package for nimblegen microarray analysis
this the session info
> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-pc-linux-gnu
locale:
[1] LC_CTYPE=fr_FR.utf8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.utf8 LC_COLLATE=fr_FR.utf8
[5] LC_MONETARY=fr_FR.utf8 LC_MESSAGES=fr_FR.utf8
[7] LC_PAPER=fr_FR.utf8 LC_NAME=fr_FR.utf8
[9] LC_ADDRESS=fr_FR.utf8 LC_TELEPHONE=fr_FR.utf8
[11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=fr_FR.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] pdInfoBuilder_1.12.0 oligo_1.12.2 oligoClasses_1.10.0
[4] affxparser_1.20.0 RSQLite_0.9-2 DBI_0.2-5
[7] JGR_1.7-2 iplots_1.1-3 JavaGD_0.5-2
[10] rJava_0.8-6 Biobase_2.8.0
loaded via a namespace (and not attached):
[1] affyio_1.16.0 Biostrings_2.16.9 IRanges_1.6.17
[4] preprocessCore_1.10.0 splines_2.11.1 tools_2.11.1
> traceback
function (x = NULL, max.lines = getOption("deparse.max.lines"))
{
if (is.null(x) && (exists(".Traceback", envir = baseenv())))
x <- get(".Traceback", envir = baseenv())
n <- length(x)
if (n == 0L)
cat(gettext("No traceback available"), "\n")
else {
for (i in 1L:n) {
label <- paste(n - i + 1L, ": ", sep = "")
m <- length(x[[i]])
if (!is.null(srcref <- attr(x[[i]], "srcref"))) {
srcfile <- attr(srcref, "srcfile")
x[[i]][m] <- paste(x[[i]][m], " at ",
basename(srcfile$filename),
"#", srcref[1L], sep = "")
}
if (m > 1)
label <- c(label, rep(substr(" ", 1L,
nchar(label, type = "w")), m - 1L))
if (is.numeric(max.lines) && max.lines > 0L && max.lines <
m) {
cat(paste(label[1L:max.lines], x[[i]][1L:max.lines],
sep = ""), sep = "\n")
cat(label[max.lines + 1L], " ...\n")
}
else cat(paste(label, x[[i]], sep = ""), sep = "\n")
}
}
invisible()
}
<environment: namespace:base="">
and the tracebck
> traceback()
7: stop("'by' must specify valid column(s)")
6: fix.by(by.x, x)
5: merge.data.frame(ndfdata, xysdata, by.x = c("X", "Y"), by.y =
c("X",
"Y"))
4: merge(ndfdata, xysdata, by.x = c("X", "Y"), by.y = c("X", "Y"))
3: parseNgsPair(object@ndfFile, object@xysFile, verbose = !quiet)
2: makePdInfoPackage(seed, destDir = ".")
1: makePdInfoPackage(seed, destDir = ".")
and this is my script :
> library(pdInfoBuilder)
> baseDir <- "/home/michael/Documents/test_2007"
> (ndf <- list.files(baseDir, pattern = ".ndf",full.names = TRUE))
[1] "/home/michael/Documents/test_2007/new2.ndf"
> (xys <- list.files(baseDir, pattern = ".xys", full.names = TRUE)[1])
[1] "/home/michael/Documents/test_2007/nobless1.xys"
> seed <- new("NgsExpressionPDInfoPkgSeed",
+ ndfFile = ndf, xysFile = xys,
+ author = "Momo Allo",
+ email = "mozemaster@gmail.com",
+ biocViews = "AnnotationData",
+ genomebuild = "LGDP",
+ organism = "Rice", species = "Oryza Sativa",
+ url = "http://www.biostat.jhsph.edu/~bcarvalh")
> makePdInfoPackage(seed, destDir = ".")
======================================================================
==========
Building annotation package for Nimblegen Expression Array
NDF: new2.ndf
XYS: nobless1.xys
======================================================================
==========
Parsing file: new2.ndf... OK
Parsing file: nobless1.xys... OK
Merging NDF and XYS files... Erreur dans fix.by(by.x, x) : 'by' must
specify
valid column(s)
so i don't understand why i've got this error, so if anybody could
help me
where is the main problem ?
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