[BioC] PdInfoBuilder for nimblegen array

Benilton Carvalho beniltoncarvalho at gmail.com
Thu Feb 25 19:57:38 CET 2010


Alex,

much easier than that (because now I know what array you're working
with) is to use the pre-made pd packages. They're going to make their
way to BioC, but in the meantime use the instructions at:

http://www.biostat.jhsph.edu/~maryee/charm/

b

On Thu, Feb 25, 2010 at 4:59 PM, Alex Rodriguez
<arodrigu1 at bsd.uchicago.edu> wrote:
> Hi Benilton,
> Here is a sample of one of the xys files:
>>head 136413_532.xys
> # software=NimbleScan HD2-beta  version=2.4.18  imagefile=./136413_532.tif
> designfile=/nfs/designs/Feinberg_HG18_Me_HX1.ndf
> designname=Feinberg_HG18_Me
> _HX1    designid=6353   date=Thu Oct 04 18:13:16 CDT 2007       border=0
> ul_x=132.271    ul_y=67.752     ur_x=2992.461   ur_y=45.954
> lr_x=3011.604   lr_
> y=3865.026      ll_x=151.111    ll_y=3886.875   score=0.169
> qcscore=0.377   locallyaligned=no       correctAstig=no Knots=  auto=no
> X       Y       SIGNAL  COUNT
> 1       1       847.78  1
> 23      1       841.11  1
> 25      1       1180.67 1
> 27      1       727.33  1
> 29      1       427.33  1
> 31      1       460.00  1
> 33      1       561.67  1
> 35      1       638.00  1
> 37      1       2622.22 1
> 39      1       463.89  1
> 41      1       479.00  1
> 43      1       4508.89 1
> 45      1       4394.44 1
> 47      1       951.56  1
> 49      1       304.89  1
>
> The rest of the xys files follow the same format, and do include NA where it
> should be.
>
> Thanks,
>
> Alex
>
>
> On 2/24/10 5:54 PM, "Benilton Carvalho" <beniltoncarvalho at gmail.com> wrote:
>
>> 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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