[BioC] PdInfoBuilder for nimblegen array

[Benilton Carvalho]

Hi Alex,

So, you're creating the XYS files yourself, right?

These files should be sorted by X/Y coordinates and the SIGNAL columns
for the control probes should be NA.

If you happen to have NimbleScan, it can create the XYS files directly
and appropriately. If you're going to create them manually, they
should follow the requirements above. Can you tell me if yours are
like this?

THanks,

b

On Wed, Feb 24, 2010 at 6:01 PM, Alex Rodriguez
<arodrigu1 at bsd.uchicago.edu> wrote:
> 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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