[BioC] error fix.by(by.x, x) in Pdinfobuilder package

[Benilton Carvalho]

How did you obtain the NDF and XYS files? (new2.ndf and nobless1.xys
do not seem as standard names for NDF/XYS files)

b

On 11 October 2010 16:38, Michael MOZAR <mozemaster at gmail.com> wrote:
> 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 at ndfFile, object at 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 at 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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>
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