[BioC] dChip LOH and copy number analysis

[Henrik Bengtsson]

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  I have a somewhat outdated document explaining this further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
>>
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>