[BioC] dChip LOH and copy number analysis

[Yu Chuan Tai]

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.

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  I have a somewhat outdated document explaining this further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