[BioC] PdInfoBuilder for nimblegen array
Alex Rodriguez
arodrigu1 at bsd.uchicago.edu
Thu Feb 25 20:08:43 CET 2010
Hi Benilton,
Sorry, I copied the wrong segment of xys files.
Here is the header of the actual xys file which is different than the
pre-made package, I think.
>head 41779702_635.xys
# software=NimbleScan version=2.5.28
imagefile=/nfs/bioinfo/production/analysis/active/21863y/41779702_635.tif
designfile=/nfs/designs/081229_HG18_Promote
r_MeDIP_HX1.ndf designname=081229_HG18_Promoter_MeDIP_HX1
designid=8567 date=Mon Dec 21 10:23:20 CST 2009 border=0
ul_x=4.500 ul_y=3.500ur_x=1050.500 ur_y=3.500 lr_x=1050.500
lr_y=1399.500 ll_x=4.500 ll_y=1399.500 score=0.000
qcscore=0.233 locallyaligned=no correctAsti
g=no Knots= auto=no
X Y Signal Count
259 1 440.00 1
465 1 468.00 1
725 1 377.00 1
797 1 453.00 1
827 1 303.00 1
859 1 399.00 1
234 2 560.00 1
440 2 2471.00 1
464 2 393.00 1
722 2 1470.00 1
730 2 300.00 1
1028 2 333.00 1
189 3 336.00 1
257 3 392.00 1
379 3 423.00 1
437 3 299.00 1
701 3 337.00 1
811 3 522.00 1
190 4 497.00 1
334 4 362.00 1
Does this look correct?
Thanks and sorry for the confusion,
Alex
On 2/25/10 12:57 PM, "Benilton Carvalho" <beniltoncarvalho at gmail.com> wrote:
> 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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