[BioC] dChip LOH and copy number analysis
Yu Chuan Tai
yuchuan at stat.berkeley.edu
Wed Sep 17 01:37:48 CEST 2008
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 I have a somewhat outdated document explaining this further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
>>>>>
>>>>> _______________________________________________
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>>>>>
>>>>
>>>
>>
>
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