[BioC] PdInfoBuilder for nimblegen array
Alex Rodriguez
arodrigu1 at bsd.uchicago.edu
Thu Feb 25 17:59:19 CET 2010
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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>>
>>
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