[BioC] PdInfoBuilder for nimblegen array

[Benilton Carvalho]

Hi Alex,

what's your sessionInfo()?

Additionally, can you confirm you got the XYS files from NimbleGen or
NimbleScan?

Thank you,

benilton

On Fri, Feb 19, 2010 at 7:44 PM, Alex Rodriguez
<arodrigu1 at bsd.uchicago.edu> wrote:
> Hi,
> I am new using pdInfoBuilder, so I may be missing something. I am trying to
> use pdInfoBuilder to make an annotation package. However, I get an error
> after the makePdInfoPackage(seed, destDir = "./") command.
>
> Error in aggregate.data.frame(as.data.frame(x), ...) :
>  no rows to aggregate
>
>  Has anybody encountered this message?
>
> Thanks!,
>
> Alex
>
> Here is my list of commands:
>
>> library(pdInfoBuilder)
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
>  Vignettes contain introductory material. To view, type
>  'openVignette()'. To cite Bioconductor, see
>  'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: RSQLite
> Loading required package: DBI
> Loading required package: affxparser
> Loading required package: oligo
> Loading required package: oligoClasses
> Loading required package: preprocessCore
> Welcome to oligo version 1.10.2
>> baseDir <- "/cchome/qichen2/Nimblegen_methylation/21863"
>> (ndf <- list.files(baseDir, pattern = "ndf", full.names = TRUE))
> [1]
> "/cchome/qichen2/Nimblegen_methylation/21863/081229_HG18_Promoter_MeDIP_HX1.
> ndf"
>> (xys <- list.files(baseDir, pattern = ".xys", full.names = TRUE)[1])
> [1] "/cchome/qichen2/Nimblegen_methylation/21863/38693602_532.xys"
>> (pos <- list.files(baseDir, pattern = ".pos", full.names = TRUE))
> [1]
> "/cchome/qichen2/Nimblegen_methylation/21863/081229_HG18_Promoter_MeDIP_HX1.
> pos"
>> seed <- new("NgsTilingPDInfoPkgSeed", ndfFile = ndf, xysFile = xys,posFile =
> pos, author = "AR", biocViews
> = "AnnotationData", genomebuild = "HG 18", organism = "Human", species =
> "Homo Sapiens")
>> makePdInfoPackage(seed, destDir = "./")
> ============================================================================
> ====
> Building annotation package for Nimblegen Tiling Array
> NDF:  081229_HG18_Promoter_MeDIP_HX1.ndf
> POS:  081229_HG18_Promoter_MeDIP_HX1.pos
> XYS:  38693602_532.xys
> ============================================================================
> ====
> Parsing file: 081229_HG18_Promoter_MeDIP_HX1.ndf ... OK
> Parsing file: 081229_HG18_Promoter_MeDIP_HX1.pos ... OK
> Merging NDF and POS files... OK
> Parsing file: 38693602_532.xys ... OK
> Error in aggregate.data.frame(as.data.frame(x), ...) :
>  no rows to aggregate
> Calls: makePdInfoPackage ... aggregate -> aggregate.default ->
> aggregate.data.frame
> In addition: Warning message:
> In is.na(ndfdata[["SIGNAL"]]) :
>  is.na() applied to non-(list or vector) of type 'NULL'
> Execution halted
>
>
>
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