[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
>>>>>
>>>>>
>>>>>
>>>>> This email is intended only for the use of the individua...{{dropped:6}}
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>
>>>
>>>
>>> This email is intended only for the use of the individual or entity to which
>>> it is addressed and may contain information that is privileged and
>>> confidential. If the reader of this email message is not the intended
>>> recipient, you are hereby notified that any dissemination, distribution, or
>>> copying of this communication is prohibited. If you have received this email
>>> in error, please notify the sender and destroy/delete all copies of the
>>> transmittal. Thank you.
>>>
>>>
>
>
>
> This email is intended only for the use of the individ...{{dropped:10}}
More information about the Bioconductor
mailing list