Thanks! I guesss the first thing I should do is to read your "HB's Guide to dChip" then :) Yu Chuan On Tue, 16 Sep 2008, Henrik Bengtsson wrote: > On Tue, Sep 16, 2008 at 4:19 PM, Yu Chuan Tai <yuchuan at="" stat.berkeley.edu=""> wrote: >> Hi Henrik, >> >> Thanks a lot for your detailed answers. Very helpful. I did checked dChip's >> manual, but when I tried, I only got an excel file containing "inferred copy >> numbers" but nothing else. I will read over your "HB's Guide to dChip" first >> and see if I can become more familiar with the software. > > Yep, what is exported to that file depends on what you display on the > screen when you do the export. That is/was the only way how to > specify if "inferred" or "raw" CNs are exported. That is pointed out > in 'HB's Guide to dChip'. > > Cheers > > Henrik > >> >> Best, >> Yu Chuan >> >> On Tue, 16 Sep 2008, Henrik Bengtsson wrote: >> >>> Wrong URL: It should be http://www.dchip.org/ and nothing else. /HB >>> >>> On Tue, Sep 16, 2008 at 4:01 PM, Henrik Bengtsson <hb at="" stat.berkeley.edu=""> >>> wrote: >>>> >>>> Hi, >>>> >>>> it is possible to export such estimates to text files from within >>>> dChip. Check the dChip manual and user forum at >>>> http://www.dchip.com/. From there it depends where you want to >>>> import it and what methods you want to use. I'll let someone else >>>> answer that. >>>> >>>> Some more FYI: >>>> AFAIK, the *low-level data* exported from dChip reflect what is in the >>>> DCP files (binary data files created by dChip). Each DCP file hold >>>> (i) raw probe data (imported from the CEL files), (ii) normalized >>>> probe data, (iii) genotype calls, (iv) unit group/probeset summaries, >>>> aka "thetas"/"chip effects", and (v) std estimates of the latter. >>>> >>>> What is actually stored in the "theta" and the "stdvs" fields may >>>> depend on what settings you used in dChip, e.g. for SNPs (theta, >>>> stdvs) holds (theta_A,theta_B) if you tell dChip to fit >>>> allele-specific estimates and the stdvs is not stored anywhere, but if >>>> you choose to sum PMA+PMB while fitting, they hold what their names >>>> says. This is important to known/understand also when you choose to >>>> export estimates to text files, because the exported files will also >>>> have these constraints (although the column names says something >>>> else). I have a somewhat outdated document explaining this further >>>> with some plots showing how different settings change what is stored >>>> in DCP/exported; >>>> >>>> HB's Guide to dChip >>>> URL: http://docs.google.com/Doc?id=dddzqd53_28gzfkkg >>>> >>>> If you're still with me, you'll note that at the end of this document, >>>> I also have some notes on how to export "copy number and log ratio >>>> estimates". >>>> >>>> FYI: I'm developing a low-level package 'dChipIO' for reading dChip's >>>> DCP (and CDF.bin) binary files such that you do not have to export >>>> (and import) text files, but can work with the DCP files directly >>>> (faster, saves disk space, and removes one step of confusion). It >>>> provides an API similar what 'affxparser' provides for Affymetrix >>>> files. The dChipIO package can be installed as: >>>> >>>> source("http://www.braju.com/R/hbLite.R"); >>>> hbLite("dChipIO"); >>>> >>>> From example(readDcp): >>>>> >>>>> library("dChipIO"); >>>>> path <- system.file("exData", package="dChipIO"); >>>>> filename <- "Test3-1-121502.dcp"; >>>>> pathname <- file.path(path, filename); >>>>> data <- readDcp(pathname) >>>>> str(data) >>>> >>>> List of 7 >>>> $ header :List of 12 >>>> ..$ Header : chr "" >>>> ..$ Format : int 4 >>>> ..$ Normalized : logi FALSE >>>> ..$ ThetaValid : logi FALSE >>>> ..$ Median : int 143 >>>> ..$ MaxInten : int 0 >>>> ..$ CellDim : int 126 >>>> ..$ DatFile : chr "C:\\Documents and >>>> >>>> Settings\\hb\\braju.com.R\\aroma.affymetrix\\reengineeringdChip\\ annotationData\\Test3-1-121502.CEL" >>>> ..$ BaselineFile : chr "" >>>> ..$ ArrayOutlierPct : num 0 >>>> ..$ SingleOutlierPct: num 0 >>>> ..$ PresencePct : num 0 >>>> $ rawIntensities : int [1:15876] 190 11184 181 11144 154 162 >>>> 10141 158 10507 140 ... >>>> $ normalizedIntensities: int [1:15876] 376 1082 4800 1404 0 0 0 0 0 0 >>>> ... >>>> $ calls : raw [1:345] 00 00 00 00 ... >>>> $ thetas : num [1:345] 2.19e-36 5.01e-40 2.81e+20 >>>> 7.01e-45 5.51e-40 ... >>>> $ thetaStds : num [1:345] 1.20e-35 6.43e-39 7.01e-45 >>>> 5.86e-40 7.13e+31 ... >>>> $ excludes : int [1:345] 4 327753 4849734 5439488 6 >>>> 488564 1667694592 7 524391 6815828 ... >>>> >>>> This give you an idea what's in the DCP files/gets exported. >>>> >>>> Cheers >>>> >>>> /Henrik >>>> >>>> On Tue, Sep 16, 2008 at 1:59 PM, Yu Chuan Tai <yuchuan at="" stat.berkeley.edu=""> >>>> wrote: >>>>> >>>>> Hi all, >>>>> >>>>> Just wonder if anyone knows how to export the results from LOH, copy >>>>> numbers, and major copy proportions (MCP) analyses from dChip? >>>>> I am new to the sofware and haven't found the functions for these. >>>>> >>>>> Thanks! >>>>> Yu Chuan >>>>> >>>>> _______________________________________________ >>>>> 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 >>>>> >>>> >>> >> >