Re: [aroma.affymetrix] Could not loacate CystoScanHD_Array annotation

2015-01-07 Thread Chengyu Liu 
Thanks，it is working now. I am sorry for the late reply. I was on holidays 
and just back.
About ACS, UGP and UFL, are they necessary for the copy number calls?

Br,


On Monday, December 15, 2014 8:25:17 PM UTC+2, Henrik Bengtsson wrote:

 On Mon, Dec 15, 2014 at 8:38 AM, Chengyu Liu chengyu...@gmail.com 
 javascript: wrote: 
  Thanks. 
  
  I tried to bypass the NetAffx issue. I downloaded the cdf file from 
 aroma 
  (
 http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/) 

  and Affymetrix website. 
  Annotation file can be located, but following functions does not work. 
 It 
  was my first time to deal with aroma.afymetrix package. Maybe I was 
 using 
  wrong way. 

 Regarding this  one: Download (and gunzip) also the ACS, UGP and UFL 
 files and place them in annotationData/chipTypes/CytoScanHD_Array/ and 
 then the following will work. 

 /Henrik 

  
  Any comments are appreciated. 
  
  cdf - AffymetrixCdfFile$byChipType('CytoScanHD_Array'); 
  print(cdf) 
  AffymetrixCdfFile: 
  Path: annotationData/chipTypes/CytoScanHD_Array 
  Filename: CytoScanHD_Array.cdf 
  File size: 612.27 MB (642007896 bytes) 
  Chip type: CytoScanHD_Array 
  RAM: 0.00MB 
  File format: v4 (binary; XDA) 
  Dimension: 2572x2680 
  Number of cells: 6892960 
  Number of units: 2822125 
  Cells per unit: 2.44 
  Number of QC units: 4 
  
 gi - getGenomeInformation(cdf) 
  [2014-12-15 18:28:32] Exception: Failed to retrieve genome information 
 for 
  this chip type: CytoScanHD_Array 
  
at #02. getGenomeInformation.AffymetrixCdfFile(cdf) 
- getGenomeInformation.AffymetrixCdfFile() is in environment 
  'aroma.affymetrix' 
  
at #01. getGenomeInformation(cdf) 
- getGenomeInformation() is in environment 'aroma.affymetrix' 
  
  Error: Failed to retrieve genome information for this chip type: 
  CytoScanHD_Array 
  
 si - getSnpInformation(cdf) 
  20141215 18:31:41|Defining DChipSnpInformation from chip type... 
  20141215 18:31:41| Chip type: CytoScanHD_Array 
  20141215 18:31:41| Version: 
  20141215 18:31:41| Located pathname: 
  20141215 18:31:41|Defining DChipSnpInformation from chip type...done 
  [2014-12-15 18:31:41] Exception: Failed to retrieve SNP information for 
 this 
  chip type: CytoScanHD_Array 
  
at #02. getSnpInformation.AffymetrixCdfFile(cdf) 
- getSnpInformation.AffymetrixCdfFile() is in environment 
  'aroma.affymetrix' 
  
at #01. getSnpInformation(cdf) 
- getSnpInformation() is in environment 'aroma.affymetrix' 
  
  Error: Failed to retrieve SNP information for this chip type: 
  CytoScanHD_Array 
  
 acs - AromaCellSequenceFile$byChipType(getChipType(cdf, 
 fullname=FALSE)) 
  [2014-12-15 18:31:50] Exception: Failed to create AromaCellSequenceFile 
  object. Could not locate an annotation data file for chip type 
  'CytoScanHD_Array' (without requiring any tags) and with filename 
 extension 
  'acs'. 
  
at #03. byChipType.AromaMicroarrayTabularBinaryFile(static, ...) 
- byChipType.AromaMicroarrayTabularBinaryFile() is in 
 environment 
  'aroma.core' 
  
at #02. byChipType(static, ...) 
- byChipType() is in environment 'aroma.core' 
- originating from 'text' 
  
at #01. AromaCellSequenceFile$byChipType(getChipType(cdf, fullname = 
  FALSE)) 
- AromaCellSequenceFile$byChipType() is local of the calling 
  function 
  
  Error: Failed to create AromaCellSequenceFile object. Could not locate 
 an 
  annotation data file for chip type 'CytoScanHD_Array' (without requiring 
 any 
  tags) and with filename extension 'acs'. 
  
  
  On Monday, December 15, 2014 6:27:51 PM UTC+2, Henrik Bengtsson wrote: 
  
  I can reproduce this; 
  
   csv - AffymetrixNetAffxCsvFile$byChipType(chipType) 
  Error in grep(pattern, basename(files0)) : invalid 'pattern' argument 
  
  I'll investigate. 
  
  /Henrik 
  
  On Mon, Dec 15, 2014 at 5:51 AM, Chengyu Liu chengyu...@gmail.com 
 wrote: 
   Hi, 
   
   I am trying to read annotation file of CytoScanHD_Array, but somehow 
 it 
   could not locate it. 
   
   I followed the tutorial in the web 
   http://aroma-project.org/setup/annotationData/. I am using NetAffx 
   Annotation Files (I could not find CDF file) . 
   I created folder annotationData/chipTypes/CytoScanHD_Array/NetAffx/ 
  and 
   put 
   annotation file CytoScanHD_Array_annot.csv there. 
   
   I ran AffymetrixNetAffxCsvFile$byChipType(CytoScanHD_Array) at 
 parent 
   directory of annotationData. 
   
   It gave error Error in grep(pattern, basename(files0)) : invalid 
   'pattern' 
   argument 
   
   Does anyone know what was wrong ? 
   
   Br, 
   C.Y 
   
   -- 
   -- 
   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

Re: [aroma.affymetrix] Could not loacate CystoScanHD_Array annotation

2015-01-07 Thread Henrik Bengtsson 
On Jan 7, 2015 3:43 AM, Chengyu Liu chengyu.liu...@gmail.com wrote:

 Thanks，it is working now. I am sorry for the late reply. I was on
holidays and just back.
 About ACS, UGP and UFL, are they necessary for the copy number calls?

Yes.

Henrik


 Br,


 On Monday, December 15, 2014 8:25:17 PM UTC+2, Henrik Bengtsson wrote:

 On Mon, Dec 15, 2014 at 8:38 AM, Chengyu Liu chengyu...@gmail.com
wrote:
  Thanks.
 
  I tried to bypass the NetAffx issue. I downloaded the cdf file from
aroma
  (
http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/)

  and Affymetrix website.
  Annotation file can be located, but following functions does not work.
It
  was my first time to deal with aroma.afymetrix package. Maybe I was
using
  wrong way.

 Regarding this  one: Download (and gunzip) also the ACS, UGP and UFL
 files and place them in annotationData/chipTypes/CytoScanHD_Array/ and
 then the following will work.

 /Henrik

 
  Any comments are appreciated.
 
  cdf - AffymetrixCdfFile$byChipType('CytoScanHD_Array');
  print(cdf)
  AffymetrixCdfFile:
  Path: annotationData/chipTypes/CytoScanHD_Array
  Filename: CytoScanHD_Array.cdf
  File size: 612.27 MB (642007896 bytes)
  Chip type: CytoScanHD_Array
  RAM: 0.00MB
  File format: v4 (binary; XDA)
  Dimension: 2572x2680
  Number of cells: 6892960
  Number of units: 2822125
  Cells per unit: 2.44
  Number of QC units: 4
 
 gi - getGenomeInformation(cdf)
  [2014-12-15 18:28:32] Exception: Failed to retrieve genome information
for
  this chip type: CytoScanHD_Array
 
at #02. getGenomeInformation.AffymetrixCdfFile(cdf)
- getGenomeInformation.AffymetrixCdfFile() is in environment
  'aroma.affymetrix'
 
at #01. getGenomeInformation(cdf)
- getGenomeInformation() is in environment
'aroma.affymetrix'
 
  Error: Failed to retrieve genome information for this chip type:
  CytoScanHD_Array
 
 si - getSnpInformation(cdf)
  20141215 18:31:41|Defining DChipSnpInformation from chip type...
  20141215 18:31:41| Chip type: CytoScanHD_Array
  20141215 18:31:41| Version:
  20141215 18:31:41| Located pathname:
  20141215 18:31:41|Defining DChipSnpInformation from chip type...done
  [2014-12-15 18:31:41] Exception: Failed to retrieve SNP information
for this
  chip type: CytoScanHD_Array
 
at #02. getSnpInformation.AffymetrixCdfFile(cdf)
- getSnpInformation.AffymetrixCdfFile() is in environment
  'aroma.affymetrix'
 
at #01. getSnpInformation(cdf)
- getSnpInformation() is in environment 'aroma.affymetrix'
 
  Error: Failed to retrieve SNP information for this chip type:
  CytoScanHD_Array
 
 acs - AromaCellSequenceFile$byChipType(getChipType(cdf,
fullname=FALSE))
  [2014-12-15 18:31:50] Exception: Failed to create
AromaCellSequenceFile
  object. Could not locate an annotation data file for chip type
  'CytoScanHD_Array' (without requiring any tags) and with filename
extension
  'acs'.
 
at #03. byChipType.AromaMicroarrayTabularBinaryFile(static, ...)
- byChipType.AromaMicroarrayTabularBinaryFile() is in
environment
  'aroma.core'
 
at #02. byChipType(static, ...)
- byChipType() is in environment 'aroma.core'
- originating from 'text'
 
at #01. AromaCellSequenceFile$byChipType(getChipType(cdf, fullname =
  FALSE))
- AromaCellSequenceFile$byChipType() is local of the calling
  function
 
  Error: Failed to create AromaCellSequenceFile object. Could not locate
an
  annotation data file for chip type 'CytoScanHD_Array' (without
requiring any
  tags) and with filename extension 'acs'.
 
 
  On Monday, December 15, 2014 6:27:51 PM UTC+2, Henrik Bengtsson wrote:
 
  I can reproduce this;
 
   csv - AffymetrixNetAffxCsvFile$byChipType(chipType)
  Error in grep(pattern, basename(files0)) : invalid 'pattern' argument
 
  I'll investigate.
 
  /Henrik
 
  On Mon, Dec 15, 2014 at 5:51 AM, Chengyu Liu chengyu...@gmail.com
wrote:
   Hi,
  
   I am trying to read annotation file of CytoScanHD_Array, but
somehow it
   could not locate it.
  
   I followed the tutorial in the web
   http://aroma-project.org/setup/annotationData/. I am using NetAffx
   Annotation Files (I could not find CDF file) .
   I created folder annotationData/chipTypes/CytoScanHD_Array/NetAffx/
 and
   put
   annotation file CytoScanHD_Array_annot.csv there.
  
   I ran AffymetrixNetAffxCsvFile$byChipType(CytoScanHD_Array) at
parent
   directory of annotationData.
  
   It gave error Error in grep(pattern, basename(files0)) : invalid
   'pattern'
   argument
  
   Does anyone know what was wrong ?
  
   Br,
   C.Y
  
   --
   --
   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/.

Re: [aroma.affymetrix] Could not loacate CystoScanHD_Array annotation

2014-12-15 Thread Chengyu Liu 
Thanks.

I tried to bypass the NetAffx issue. I downloaded the cdf file from aroma 
(http://www.aroma-project.org/data/annotationData/chipTypes/CytoScanHD_Array/) 
and Affymetrix website.
Annotation file can be located, but following functions does not work. It 
was my first time to deal with aroma.afymetrix package. Maybe I was using 
wrong way.

Any comments are appreciated. 

 cdf - AffymetrixCdfFile$byChipType('CytoScanHD_Array');
 print(cdf)
AffymetrixCdfFile:
Path: annotationData/chipTypes/CytoScanHD_Array
Filename: CytoScanHD_Array.cdf
File size: 612.27 MB (642007896 bytes)
Chip type: CytoScanHD_Array
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 2822125
Cells per unit: 2.44
Number of QC units: 4

gi - getGenomeInformation(cdf)
[2014-12-15 18:28:32] Exception: Failed to retrieve genome information for 
this chip type: CytoScanHD_Array

  at #02. getGenomeInformation.AffymetrixCdfFile(cdf)
  - getGenomeInformation.AffymetrixCdfFile() is in environment 
'aroma.affymetrix'

  at #01. getGenomeInformation(cdf)
  - getGenomeInformation() is in environment 'aroma.affymetrix'

Error: Failed to retrieve genome information for this chip type: 
CytoScanHD_Array

si - getSnpInformation(cdf)
20141215 18:31:41|Defining DChipSnpInformation from chip type...
20141215 18:31:41| Chip type: CytoScanHD_Array
20141215 18:31:41| Version:
20141215 18:31:41| Located pathname:
20141215 18:31:41|Defining DChipSnpInformation from chip type...done
[2014-12-15 18:31:41] Exception: Failed to retrieve SNP information for 
this chip type: CytoScanHD_Array
 
  at #02. getSnpInformation.AffymetrixCdfFile(cdf)
  - getSnpInformation.AffymetrixCdfFile() is in environment 
'aroma.affymetrix'
 
  at #01. getSnpInformation(cdf)
  - getSnpInformation() is in environment 'aroma.affymetrix'
 
Error: Failed to retrieve SNP information for this chip type: 
CytoScanHD_Array

acs - AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE))
[2014-12-15 18:31:50] Exception: Failed to create AromaCellSequenceFile 
object. Could not locate an annotation data file for chip type 
'CytoScanHD_Array' (without requiring any tags) and with filename extension 
'acs'.

  at #03. byChipType.AromaMicroarrayTabularBinaryFile(static, ...)
  - byChipType.AromaMicroarrayTabularBinaryFile() is in environment 
'aroma.core'

  at #02. byChipType(static, ...)
  - byChipType() is in environment 'aroma.core'
  - originating from 'text'

  at #01. AromaCellSequenceFile$byChipType(getChipType(cdf, fullname = 
FALSE))
  - AromaCellSequenceFile$byChipType() is local of the calling 
function

Error: Failed to create AromaCellSequenceFile object. Could not locate an 
annotation data file for chip type 'CytoScanHD_Array' (without requiring 
any tags) and with filename extension 'acs'.


On Monday, December 15, 2014 6:27:51 PM UTC+2, Henrik Bengtsson wrote:

 I can reproduce this; 

  csv - AffymetrixNetAffxCsvFile$byChipType(chipType) 
 Error in grep(pattern, basename(files0)) : invalid 'pattern' argument 

 I'll investigate. 

 /Henrik 

 On Mon, Dec 15, 2014 at 5:51 AM, Chengyu Liu chengyu...@gmail.com 
 javascript: wrote: 
  Hi, 
  
  I am trying to read annotation file of CytoScanHD_Array, but somehow it 
  could not locate it. 
  
  I followed the tutorial in the web 
  http://aroma-project.org/setup/annotationData/. I am using NetAffx 
  Annotation Files (I could not find CDF file) . 
  I created folder annotationData/chipTypes/CytoScanHD_Array/NetAffx/  and 
 put 
  annotation file CytoScanHD_Array_annot.csv there. 
  
  I ran AffymetrixNetAffxCsvFile$byChipType(CytoScanHD_Array) at parent 
  directory of annotationData. 
  
  It gave error Error in grep(pattern, basename(files0)) : invalid 
 'pattern' 
  argument 
  
  Does anyone know what was wrong ? 
  
  Br, 
  C.Y 
  
  -- 
  -- 
  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 
 javascript: 
  To unsubscribe and other options, go to 
 http://www.aroma-project.org/forum/ 
  
  --- 
  You received this message because you are subscribed to the Google 
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  To unsubscribe from this group and stop receiving emails from it, send 
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  email to aroma-affymetr...@googlegroups.com javascript:. 
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-- 
-- 
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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