[BioC] PdInfoBuilder for nimblegen array

[Alex Rodriguez]

Hi Benilton,
Thanks for your prompt reply!
The .xys file were created from .pair file which are from NimbleScan.

Here is my output for sessionInfo():

> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] pdInfoBuilder_1.10.1 oligo_1.10.2         preprocessCore_1.8.0
[4] oligoClasses_1.8.0   affxparser_1.18.0    RSQLite_0.8-2
[7] DBI_0.2-5            Biobase_2.6.1

loaded via a namespace (and not attached):
[1] affyio_1.14.0      Biostrings_2.14.12 IRanges_1.4.11     splines_2.10.1

Thanks for your input!

Alex

On 2/23/10 4:52 PM, "Benilton Carvalho" <beniltoncarvalho at gmail.com> wrote:

> 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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