[BioC] dChip LOH and copy number analysis
hb at stat.berkeley.edu
Wed Sep 17 01:12:01 CEST 2008
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:
> 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 I have a somewhat outdated document explaining this further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
> 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:
> From example(readDcp):
>> path <- system.file("exData", package="dChipIO");
>> filename <- "Test3-1-121502.dcp";
>> pathname <- file.path(path, filename);
>> data <- readDcp(pathname)
> 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
> ..$ 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.
> 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.
>> Yu Chuan
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
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