Re: [aroma.affymetrix] How to apply TumorBoost to Illumina data?

2012-09-14 Thread Reed
Thanks, Henrik. I have used small chr1 data to test low level API. 

Can I run the all chromosome's data at one go? In case of preparing a 
single input datafile for all chromosome, how to take care about the 
chromosomal position.

Reed. 

On Thursday, September 13, 2012 9:36:34 PM UTC+5:30, Henrik Bengtsson wrote:

 On Thu, Sep 13, 2012 at 6:11 AM, Reed ghos...@gmail.com javascript: 
 wrote: 
  Dear Henrik, 
  
  How do I convert illumina BAF, LRR to the bin format. 

 For me bin means binary.  If you use the low-level API there is no 
 need to create binary files; just read the Illumina BAF (and LRR) data 
 into memory in, say, a data frame and then pass those values to 
 normalizeTumorBoost(). 

 /Henrik 

  
  Please help. 
  
  Reed 
  
  
  On Wednesday, September 12, 2012 8:14:21 PM UTC+5:30, Henrik Bengtsson 
  wrote: 
  
  Hi, 
  
  On Sun, Sep 9, 2012 at 10:18 PM, Unyanee Poolsap uny...@gmail.com 
 wrote: 
   Hello, 
   
   I have a question regarding to TumorBoost. 
   I have data from Affymetrix (GenomeWideSNP_6) and Illumina 
 (Omni1-Quad) 
   for 
   the same set of samples. 
   I want to do normalization of CNV for the data from both platforms 
   for the purpose of comparison and false positive cut. 
   
   I can follow the vignettes 
   (http://aroma-project.org/vignettes/tumorboost-highlevel) 
   for applying TumorBoost on data from Affymetrix. 
   However, I have no idea how to apply it to the data from Illumina. 
   I can export BAF, LRR, and other information from Illumina's 
   GenomeStudio in 
   a text file format, using Report Wizard. 
   It seems that TumorBoost requires binary format of BAF and genotype 
 call 
   (i.e., *.asb and *.acf respectively). 
   How can I make such binary files from the text file? 
  
  Before anything else, have you considered the low-level API to 
 TumorBoost? 
  
http://aroma-project.org/vignettes/tumorboost-lowlevel 
  
  That operates on basic R data types such as vectors and matrices. 
  
  If you're considering doing parent-specific segmentation, you may also 
  be interested in Paired PSCBS (which does TumorBoost for you).  Have a 
  a look at the 'Paired PSCBS' vignette; 
  
http://cran.r-project.org/web/packages/PSCBS/ 
  
  If you're still interested in aroma-level API to TumorBoost, i.e. 
  TumorBoostNormalization, it is possible to create your own *.asb 
  binary data files containing TCN and BAF.  You'll then also need to be 
  able to setup UGP annotation data files (for genomic positions).  (The 
  *.acf genotype file can be obtained on the fly).  However, if you 
  don't really need this, I recommend to hold back on this one, because 
  in the future there may be easier ways to do this. 
  
  /Henrik 
  
   
   Thank you. 
   
   -- 
   When reporting problems on aroma.affymetrix, make sure 1) to run the 
   latest 
   version of the package, 2) to report the output of sessionInfo() and 
   traceback(), and 3) to post a complete code example. 
   
   
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-- 
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version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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Re: [aroma.affymetrix] How to apply TumorBoost to Illumina data?

2012-09-14 Thread Henrik Bengtsson
Hi.

On Fri, Sep 14, 2012 at 3:23 AM, Reed ghosh...@gmail.com wrote:
 Thanks, Henrik. I have used small chr1 data to test low level API.

 Can I run the all chromosome's data at one go? In case of preparing a single
 input datafile for all chromosome, how to take care about the chromosomal
 position.

Yes, nothing in the TumorBoost method makes use of genomic locations
(nor chromosome or position); it normalizes tumor BAFs given the
corresponding matched normal BAFs for SNPs independently of each
other.

/H


 Reed.

 On Thursday, September 13, 2012 9:36:34 PM UTC+5:30, Henrik Bengtsson wrote:

 On Thu, Sep 13, 2012 at 6:11 AM, Reed ghos...@gmail.com wrote:
  Dear Henrik,
 
  How do I convert illumina BAF, LRR to the bin format.

 For me bin means binary.  If you use the low-level API there is no
 need to create binary files; just read the Illumina BAF (and LRR) data
 into memory in, say, a data frame and then pass those values to
 normalizeTumorBoost().

 /Henrik

 
  Please help.
 
  Reed
 
 
  On Wednesday, September 12, 2012 8:14:21 PM UTC+5:30, Henrik Bengtsson
  wrote:
 
  Hi,
 
  On Sun, Sep 9, 2012 at 10:18 PM, Unyanee Poolsap uny...@gmail.com
  wrote:
   Hello,
  
   I have a question regarding to TumorBoost.
   I have data from Affymetrix (GenomeWideSNP_6) and Illumina
   (Omni1-Quad)
   for
   the same set of samples.
   I want to do normalization of CNV for the data from both platforms
   for the purpose of comparison and false positive cut.
  
   I can follow the vignettes
   (http://aroma-project.org/vignettes/tumorboost-highlevel)
   for applying TumorBoost on data from Affymetrix.
   However, I have no idea how to apply it to the data from Illumina.
   I can export BAF, LRR, and other information from Illumina's
   GenomeStudio in
   a text file format, using Report Wizard.
   It seems that TumorBoost requires binary format of BAF and genotype
   call
   (i.e., *.asb and *.acf respectively).
   How can I make such binary files from the text file?
 
  Before anything else, have you considered the low-level API to
  TumorBoost?
 
http://aroma-project.org/vignettes/tumorboost-lowlevel
 
  That operates on basic R data types such as vectors and matrices.
 
  If you're considering doing parent-specific segmentation, you may also
  be interested in Paired PSCBS (which does TumorBoost for you).  Have a
  a look at the 'Paired PSCBS' vignette;
 
http://cran.r-project.org/web/packages/PSCBS/
 
  If you're still interested in aroma-level API to TumorBoost, i.e.
  TumorBoostNormalization, it is possible to create your own *.asb
  binary data files containing TCN and BAF.  You'll then also need to be
  able to setup UGP annotation data files (for genomic positions).  (The
  *.acf genotype file can be obtained on the fly).  However, if you
  don't really need this, I recommend to hold back on this one, because
  in the future there may be easier ways to do this.
 
  /Henrik
 
  
   Thank you.
  
   --
   When reporting problems on aroma.affymetrix, make sure 1) to run the
   latest
   version of the package, 2) to report the output of sessionInfo() and
   traceback(), and 3) to post a complete code example.
  
  
   You received this message because you are subscribed to the Google
   Groups
   aroma.affymetrix group with website http://www.aroma-project.org/.
   To post to this group, send email to aroma-af...@googlegroups.com
   To unsubscribe and other options, go to
   http://www.aroma-project.org/forum/

 --
 When reporting problems on aroma.affymetrix, make sure 1) to run the latest
 version of the package, 2) to report the output of sessionInfo() and
 traceback(), and 3) to post a complete code example.


 You received this message because you are subscribed to the Google Groups
 aroma.affymetrix group with website http://www.aroma-project.org/.
 To post to this group, send email to aroma-affymetrix@googlegroups.com

 To unsubscribe and other options, go to http://www.aroma-project.org/forum/

-- 
When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


You received this message because you are subscribed to the Google Groups 
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Re: [aroma.affymetrix] How to apply TumorBoost to Illumina data?

2012-09-13 Thread Reed
Dear Henrik,

How do I convert illumina BAF, LRR to the bin format. 

Please help.

Reed

On Wednesday, September 12, 2012 8:14:21 PM UTC+5:30, Henrik Bengtsson 
wrote:

 Hi, 

 On Sun, Sep 9, 2012 at 10:18 PM, Unyanee Poolsap 
 uny...@gmail.comjavascript: 
 wrote: 
  Hello, 
  
  I have a question regarding to TumorBoost. 
  I have data from Affymetrix (GenomeWideSNP_6) and Illumina (Omni1-Quad) 
 for 
  the same set of samples. 
  I want to do normalization of CNV for the data from both platforms 
  for the purpose of comparison and false positive cut. 
  
  I can follow the vignettes 
  (http://aroma-project.org/vignettes/tumorboost-highlevel) 
  for applying TumorBoost on data from Affymetrix. 
  However, I have no idea how to apply it to the data from Illumina. 
  I can export BAF, LRR, and other information from Illumina's 
 GenomeStudio in 
  a text file format, using Report Wizard. 
  It seems that TumorBoost requires binary format of BAF and genotype call 
  (i.e., *.asb and *.acf respectively). 
  How can I make such binary files from the text file? 

 Before anything else, have you considered the low-level API to TumorBoost? 

   http://aroma-project.org/vignettes/tumorboost-lowlevel 

 That operates on basic R data types such as vectors and matrices. 

 If you're considering doing parent-specific segmentation, you may also 
 be interested in Paired PSCBS (which does TumorBoost for you).  Have a 
 a look at the 'Paired PSCBS' vignette; 

   http://cran.r-project.org/web/packages/PSCBS/ 

 If you're still interested in aroma-level API to TumorBoost, i.e. 
 TumorBoostNormalization, it is possible to create your own *.asb 
 binary data files containing TCN and BAF.  You'll then also need to be 
 able to setup UGP annotation data files (for genomic positions).  (The 
 *.acf genotype file can be obtained on the fly).  However, if you 
 don't really need this, I recommend to hold back on this one, because 
 in the future there may be easier ways to do this. 

 /Henrik 

  
  Thank you. 
  
  -- 
  When reporting problems on aroma.affymetrix, make sure 1) to run the 
 latest 
  version of the package, 2) to report the output of sessionInfo() and 
  traceback(), and 3) to post a complete code example. 
  
  
  You received this message because you are subscribed to the Google 
 Groups 
  aroma.affymetrix group with website http://www.aroma-project.org/. 
  To post to this group, send email to 
  aroma-af...@googlegroups.comjavascript: 
  To unsubscribe and other options, go to 
 http://www.aroma-project.org/forum/ 


-- 
When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


You received this message because you are subscribed to the Google Groups 
aroma.affymetrix group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/


Re: [aroma.affymetrix] How to apply TumorBoost to Illumina data?

2012-09-13 Thread Henrik Bengtsson
On Thu, Sep 13, 2012 at 6:11 AM, Reed ghosh...@gmail.com wrote:
 Dear Henrik,

 How do I convert illumina BAF, LRR to the bin format.

For me bin means binary.  If you use the low-level API there is no
need to create binary files; just read the Illumina BAF (and LRR) data
into memory in, say, a data frame and then pass those values to
normalizeTumorBoost().

/Henrik


 Please help.

 Reed


 On Wednesday, September 12, 2012 8:14:21 PM UTC+5:30, Henrik Bengtsson
 wrote:

 Hi,

 On Sun, Sep 9, 2012 at 10:18 PM, Unyanee Poolsap uny...@gmail.com wrote:
  Hello,
 
  I have a question regarding to TumorBoost.
  I have data from Affymetrix (GenomeWideSNP_6) and Illumina (Omni1-Quad)
  for
  the same set of samples.
  I want to do normalization of CNV for the data from both platforms
  for the purpose of comparison and false positive cut.
 
  I can follow the vignettes
  (http://aroma-project.org/vignettes/tumorboost-highlevel)
  for applying TumorBoost on data from Affymetrix.
  However, I have no idea how to apply it to the data from Illumina.
  I can export BAF, LRR, and other information from Illumina's
  GenomeStudio in
  a text file format, using Report Wizard.
  It seems that TumorBoost requires binary format of BAF and genotype call
  (i.e., *.asb and *.acf respectively).
  How can I make such binary files from the text file?

 Before anything else, have you considered the low-level API to TumorBoost?

   http://aroma-project.org/vignettes/tumorboost-lowlevel

 That operates on basic R data types such as vectors and matrices.

 If you're considering doing parent-specific segmentation, you may also
 be interested in Paired PSCBS (which does TumorBoost for you).  Have a
 a look at the 'Paired PSCBS' vignette;

   http://cran.r-project.org/web/packages/PSCBS/

 If you're still interested in aroma-level API to TumorBoost, i.e.
 TumorBoostNormalization, it is possible to create your own *.asb
 binary data files containing TCN and BAF.  You'll then also need to be
 able to setup UGP annotation data files (for genomic positions).  (The
 *.acf genotype file can be obtained on the fly).  However, if you
 don't really need this, I recommend to hold back on this one, because
 in the future there may be easier ways to do this.

 /Henrik

 
  Thank you.
 
  --
  When reporting problems on aroma.affymetrix, make sure 1) to run the
  latest
  version of the package, 2) to report the output of sessionInfo() and
  traceback(), and 3) to post a complete code example.
 
 
  You received this message because you are subscribed to the Google
  Groups
  aroma.affymetrix group with website http://www.aroma-project.org/.
  To post to this group, send email to aroma-af...@googlegroups.com
  To unsubscribe and other options, go to
  http://www.aroma-project.org/forum/

-- 
When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


You received this message because you are subscribed to the Google Groups 
aroma.affymetrix group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/


Re: [aroma.affymetrix] How to apply TumorBoost to Illumina data?

2012-09-12 Thread Henrik Bengtsson
Hi,

On Sun, Sep 9, 2012 at 10:18 PM, Unyanee Poolsap unya...@gmail.com wrote:
 Hello,

 I have a question regarding to TumorBoost.
 I have data from Affymetrix (GenomeWideSNP_6) and Illumina (Omni1-Quad) for
 the same set of samples.
 I want to do normalization of CNV for the data from both platforms
 for the purpose of comparison and false positive cut.

 I can follow the vignettes
 (http://aroma-project.org/vignettes/tumorboost-highlevel)
 for applying TumorBoost on data from Affymetrix.
 However, I have no idea how to apply it to the data from Illumina.
 I can export BAF, LRR, and other information from Illumina's GenomeStudio in
 a text file format, using Report Wizard.
 It seems that TumorBoost requires binary format of BAF and genotype call
 (i.e., *.asb and *.acf respectively).
 How can I make such binary files from the text file?

Before anything else, have you considered the low-level API to TumorBoost?

  http://aroma-project.org/vignettes/tumorboost-lowlevel

That operates on basic R data types such as vectors and matrices.

If you're considering doing parent-specific segmentation, you may also
be interested in Paired PSCBS (which does TumorBoost for you).  Have a
a look at the 'Paired PSCBS' vignette;

  http://cran.r-project.org/web/packages/PSCBS/

If you're still interested in aroma-level API to TumorBoost, i.e.
TumorBoostNormalization, it is possible to create your own *.asb
binary data files containing TCN and BAF.  You'll then also need to be
able to setup UGP annotation data files (for genomic positions).  (The
*.acf genotype file can be obtained on the fly).  However, if you
don't really need this, I recommend to hold back on this one, because
in the future there may be easier ways to do this.

/Henrik


 Thank you.

 --
 When reporting problems on aroma.affymetrix, make sure 1) to run the latest
 version of the package, 2) to report the output of sessionInfo() and
 traceback(), and 3) to post a complete code example.


 You received this message because you are subscribed to the Google Groups
 aroma.affymetrix group with website http://www.aroma-project.org/.
 To post to this group, send email to aroma-affymetrix@googlegroups.com
 To unsubscribe and other options, go to http://www.aroma-project.org/forum/

-- 
When reporting problems on aroma.affymetrix, make sure 1) to run the latest 
version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


You received this message because you are subscribed to the Google Groups 
aroma.affymetrix group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/