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
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 I have a somewhat outdated document explaining this further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\annot
ationData\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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
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\ann
otationData\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
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
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\an
notationData\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
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>
>
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\a
nnotationData\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
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>
>>
>
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
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>>
http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>>
>>>
>>
>