Re: [aroma.affymetrix] Error in cbs segmentation crmav2

2013-05-23 Thread ysapkota 
Hi Henrik,

With the update, it is actually working now. Thank you for your help.

Cheers,
Yadav

On Wednesday, May 22, 2013 5:13:43 PM UTC-6, Henrik Bengtsson wrote:

 Hi Yadav, 

 thanks for reporting on this.  It to me a while to reproduce it.  A 
 quick fix would be to explicitly load the R.cache package, which is 
 the package that defines that missing getChecksum().  However, I've 
 fixed this in aroma.core v2.9.2, so you update the error should go 
 away.  Update as usual by: 

 source(http://aroma-project.org/hbLite.R;); 
 hbInstall(aroma.affymetrix); 

 Let me know if this solves you problem. 

 Henrik 


 On Wed, May 22, 2013 at 10:10 AM,  ysap...@ualberta.ca javascript: 
 wrote: 
  Hello, 
  
  I am running crmav2 to analyze the copy number data for 680 samples. I 
 setup 
  a CBS model but I can not actually do the segmentation and keep on 
 getting 
  the following. Any help in this regard would be much appreciated. 
  
  print(sm) 
  CbsModel: 
  Name: caseControl 
  Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired 
  Chip type (virtual): GenomeWideSNP_6 
  Path: 
  
 cbsData/caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired/GenomeWideSNP_6 

  Number of chip types: 1 
  Sample  reference file pairs: 
  Chip type #1 ('GenomeWideSNP_6') of 1: 
  Sample data set: 
  AromaUnitTotalCnBinarySet: 
  Name: caseControl 
  Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY 
  Full name: caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY 
  Number of files: 680 
  Names: 1_BM01-1_BC_6.0B4_AUG_19_08_MA_0, 
  2_GT2_BC_6.0A5_AUG_07_08_MA_0, 
  2_GVMC002_NFHcontrols_6.0D3_Apr_21_09_MA_0, ..., 
  01428_MT1428_BD_6.0D11_NOV13_09_YS [680] 
  Path (to the first file): 
  
 totalAndFracBData/caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
  

  Total file size: 4880.69 MB 
  RAM: 0.86MB 
  Reference: median of samples 
  RAM: 0.00MB 
  
  fit (sm, verbose=-10) 
  Building tuple of reference sets... 
   Type of reference: median 
   No reference available. 
   Calculating average copy-number signals... 
Retrieving average unit signals across 680 arrays... 
 AromaUnitTotalCnBinaryFile: 
 Name: .average-signals-median-mad 
 Tags: 91abb70668ff3b542cb5388901c5246a 
 Full name: 
 .average-signals-median-mad,91abb70668ff3b542cb5388901c5246a 
 Pathname: 
  
 totalAndFracBData/caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/.average-signals-median-mad,91abb70668ff3b542cb5388901c5246a.asb
  

 File size: 7.18 MB (7526027 bytes) 
 RAM: 0.00 MB 
 Number of data rows: 1881415 
 File format: v1 
 Dimensions: 1881415x1 
 Column classes: double 
 Number of bytes per column: 4 
 Footer: createdOn20130521 13:55:14 
  
 MDT/createdOnplatformAffymetrix/platformchipTypeGenomeWideSNP_6,Full/chipTypesrcDetailsnbrOfFiles680/nbrOfFilescheckSum1e2e97361b53a44049c75e534a73bad1/checkSum/srcDetailsparamsmeanNamemedian/meanNamesdNamemad/sdName/params
  

 Platform: Affymetrix 
 Chip type: GenomeWideSNP_6,Full 
Retrieving average unit signals across 680 arrays...done 
   Calculating average copy-number signals...done 
  Building tuple of reference sets...done 
  Using reference tuple: 
  AromaUnitTotalCnBinarySetTuple: 
  Name: caseControl 
  Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY 
  Chip types: GenomeWideSNP_6 
  AromaUnitTotalCnBinarySet: 
  Name: caseControl 
  Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY 
  Full name: caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY 
  Number of files: 680 
  Names: .average-signals-median-mad, .average-signals-median-mad, 
  .average-signals-median-mad, ..., .average-signals-median-mad [680] 
  Path (to the first file): 
  
 totalAndFracBData/caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
  

  Total file size: 4880.62 MB 
  RAM: 0.86MB 
  RAM: 0.00MB 
  Extract DataFileMatrix... 
   Array: 1 
   Test data sets: 
   AromaUnitTotalCnBinarySetTuple: 
   Name: caseControl 
   Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY 
   Chip types: GenomeWideSNP_6 
   AromaUnitTotalCnBinarySet: 
   Name: caseControl 
   Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY 
   Full name: caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY 
   Number of files: 680 
   Names: 1_BM01-1_BC_6.0B4_AUG_19_08_MA_0, 
  2_GT2_BC_6.0A5_AUG_07_08_MA_0, 
  2_GVMC002_NFHcontrols_6.0D3_Apr_21_09_MA_0, ..., 
  01428_MT1428_BD_6.0D11_NOV13_09_YS [680] 
   Path (to the first file): 
  
 totalAndFracBData/caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
  

   Total file size: 4880.69 MB 
   RAM: 0.86MB 
   RAM: 0.00MB 
   Test data files: 
   $`GenomeWideSNP_6,Full` 
   AromaUnitTotalCnBinaryFile: 
   Name: 1_BM01-1_BC_6.0B4_AUG_19_08_MA_0 
   Tags: total 
   Full name: 1_BM01-1_BC_6.0B4_AUG_19_08_MA_0,total 
   Pathname: 
  
 totalAndFracBData/caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/1_BM01-1_BC_6.0B4_AUG_19_08_MA_0,total.asb
  

   File size: 7.18 MB (7526135 bytes) 
   RAM: 0.00 MB

Re: [aroma.affymetrix] Error in cbs segmentation crmav2

2013-05-22 Thread Henrik Bengtsson 
Hi Yadav,

thanks for reporting on this.  It to me a while to reproduce it.  A
quick fix would be to explicitly load the R.cache package, which is
the package that defines that missing getChecksum().  However, I've
fixed this in aroma.core v2.9.2, so you update the error should go
away.  Update as usual by:

source(http://aroma-project.org/hbLite.R;);
hbInstall(aroma.affymetrix);

Let me know if this solves you problem.

Henrik


On Wed, May 22, 2013 at 10:10 AM,  ysapk...@ualberta.ca wrote:
 Hello,

 I am running crmav2 to analyze the copy number data for 680 samples. I setup
 a CBS model but I can not actually do the segmentation and keep on getting
 the following. Any help in this regard would be much appreciated.

 print(sm)
 CbsModel:
 Name: caseControl
 Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired
 Chip type (virtual): GenomeWideSNP_6
 Path:
 cbsData/caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY,paired/GenomeWideSNP_6
 Number of chip types: 1
 Sample  reference file pairs:
 Chip type #1 ('GenomeWideSNP_6') of 1:
 Sample data set:
 AromaUnitTotalCnBinarySet:
 Name: caseControl
 Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
 Full name: caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
 Number of files: 680
 Names: 1_BM01-1_BC_6.0B4_AUG_19_08_MA_0,
 2_GT2_BC_6.0A5_AUG_07_08_MA_0,
 2_GVMC002_NFHcontrols_6.0D3_Apr_21_09_MA_0, ...,
 01428_MT1428_BD_6.0D11_NOV13_09_YS [680]
 Path (to the first file):
 totalAndFracBData/caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
 Total file size: 4880.69 MB
 RAM: 0.86MB
 Reference: median of samples
 RAM: 0.00MB

 fit (sm, verbose=-10)
 Building tuple of reference sets...
  Type of reference: median
  No reference available.
  Calculating average copy-number signals...
   Retrieving average unit signals across 680 arrays...
AromaUnitTotalCnBinaryFile:
Name: .average-signals-median-mad
Tags: 91abb70668ff3b542cb5388901c5246a
Full name: .average-signals-median-mad,91abb70668ff3b542cb5388901c5246a
Pathname:
 totalAndFracBData/caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/.average-signals-median-mad,91abb70668ff3b542cb5388901c5246a.asb
File size: 7.18 MB (7526027 bytes)
RAM: 0.00 MB
Number of data rows: 1881415
File format: v1
Dimensions: 1881415x1
Column classes: double
Number of bytes per column: 4
Footer: createdOn20130521 13:55:14
 MDT/createdOnplatformAffymetrix/platformchipTypeGenomeWideSNP_6,Full/chipTypesrcDetailsnbrOfFiles680/nbrOfFilescheckSum1e2e97361b53a44049c75e534a73bad1/checkSum/srcDetailsparamsmeanNamemedian/meanNamesdNamemad/sdName/params
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full
   Retrieving average unit signals across 680 arrays...done
  Calculating average copy-number signals...done
 Building tuple of reference sets...done
 Using reference tuple:
 AromaUnitTotalCnBinarySetTuple:
 Name: caseControl
 Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
 Chip types: GenomeWideSNP_6
 AromaUnitTotalCnBinarySet:
 Name: caseControl
 Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
 Full name: caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
 Number of files: 680
 Names: .average-signals-median-mad, .average-signals-median-mad,
 .average-signals-median-mad, ..., .average-signals-median-mad [680]
 Path (to the first file):
 totalAndFracBData/caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
 Total file size: 4880.62 MB
 RAM: 0.86MB
 RAM: 0.00MB
 Extract DataFileMatrix...
  Array: 1
  Test data sets:
  AromaUnitTotalCnBinarySetTuple:
  Name: caseControl
  Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
  Chip types: GenomeWideSNP_6
  AromaUnitTotalCnBinarySet:
  Name: caseControl
  Tags: ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
  Full name: caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY
  Number of files: 680
  Names: 1_BM01-1_BC_6.0B4_AUG_19_08_MA_0,
 2_GT2_BC_6.0A5_AUG_07_08_MA_0,
 2_GVMC002_NFHcontrols_6.0D3_Apr_21_09_MA_0, ...,
 01428_MT1428_BD_6.0D11_NOV13_09_YS [680]
  Path (to the first file):
 totalAndFracBData/caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6
  Total file size: 4880.69 MB
  RAM: 0.86MB
  RAM: 0.00MB
  Test data files:
  $`GenomeWideSNP_6,Full`
  AromaUnitTotalCnBinaryFile:
  Name: 1_BM01-1_BC_6.0B4_AUG_19_08_MA_0
  Tags: total
  Full name: 1_BM01-1_BC_6.0B4_AUG_19_08_MA_0,total
  Pathname:
 totalAndFracBData/caseControl,ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY/GenomeWideSNP_6/1_BM01-1_BC_6.0B4_AUG_19_08_MA_0,total.asb
  File size: 7.18 MB (7526135 bytes)
  RAM: 0.00 MB
  Number of data rows: 1881415
  File format: v1
  Dimensions: 1881415x1
  Column classes: double
  Number of bytes per column: 4
  Footer: createdOn20130521 12:05:44