[BioC] dChip LOH and copy number analysis

[Henrik Bengtsson]

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  I have a somewhat outdated document explaining this further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