[BioC] dChip LOH and copy number analysis

[Henrik Bengtsson]

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  I have a somewhat outdated document explaining this further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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