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_M eDIP_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_M eDIP_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. 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