Re: [aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file

2011-08-09 Thread Pierre Neuvial
Hi,

Have you tried using extractAffyBatch, which is documented here:
http://aroma-project.org/howtos/extractAffyBatch ?
As far as I understand you will need the Bioconductor annotation
package corresponding to your chip type to be installed, ie

 source(http://www.bioconductor.org/biocLite.R;)
 biocLite(hgu133plus2cdf)

This is discussed in this thread:
http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/40e3950e52d73c1f/772e387a3163db56

Pierre

On Tue, Aug 9, 2011 at 4:34 AM, hsingjun cheung
hsingjun.ch...@gmail.com wrote:
 Hi Pierre:

 Thanks. These functions work now. Do you know how to extract the raw
 intensity for each probe ?

 On Aug 8, 5:48 pm, Pierre Neuvial pie...@stat.berkeley.edu wrote:
 Hi,

 The 'annotationData' directory should be directly in your working
 directory, as explained in the page Setup: Location of annotation
 data files:http://aroma-project.org/node/66

 In your case, you need to change the current directory to ~/experiment/ by

 setwd(~/experiment/)

 (or by starting your R session from this directory).  Then your command

 csR - AffymetrixCelSet$byName(KN01M013,chipType=HG-U133_Plus_2)

 should work.

 Best,

 Pierre

 On Mon, Aug 8, 2011 at 5:29 PM, hsingjun cheung







 hsingjun.ch...@gmail.com wrote:
  Hello:

  I searched the group but got no results ... So I want to know, how to
  extract the raw probe intensity from .CEL file?

  The file structure on my computer is like:

  ~/experiemnt/
              annotationData/
                          chipTypes/
                                 HG-U133_Plus_2/
                                            HG-U133_Plus_2.cdf
  ~/experiment/
                rawData/
                        KN01M013/
                                HG-U133_Plus_2/
                                                     KN01M013.CEL

  The .cdf file is downloaded 
  fromhttp://www.aroma-project.org/chipTypes/HG-U133_Plus_2

  When I run R under ~ directory:
  library(aroma.affymetrix)
   csR - AffymetrixCelSet$byName(KN01M013,chipType=HG-U133_Plus_2)

  I got error msg:

  Error in list(`AffymetrixCelSet$byName(KN01M013, chipType = HG-
  U133_Plus_2)` = environment,  :

  [2011-08-08 11:24:05] Exception: Could not locate a file for this chip
  type: HG-U133_Plus_2
   at throw(Exception(...))
   at throw.default(Could not locate a file for this chip type: ,
  paste(c(chipT
   at throw(Could not locate a file for this chip type: ,
  paste(c(chipType, tag
   at method(static, ...)
   at AffymetrixCdfFile$byChipType(chipType)
   at method(static, ...)
   at AffymetrixCelSet$byName(KN01M013, chipType = HG-U133_Plus_2)

  Could anyone help me figure how this error happened ? And how to do
  it  ( extract raw probe intensity ) in a right way ? Thanks

  --
  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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 --
 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/


Re: [aroma.affymetrix] Re: How to extract raw probe intensity from .CEL file

2011-08-09 Thread Mark Robinson

How about grabbing the intensities according to their index:

raw=extractMatrix(cs,cells=df$cell,verbose=verbose)

Then you'll have them matched up to the 'df' data.frame.

(Different numbers for your chip, of course)
 dim(df)
[1] 844550 16
 dim(raw)
[1] 844550 33


Mark

On Aug 10, 2011, at 12:31 AM, hsingjun cheung wrote:

 Hi Mark:
 
 My idea is how we could know the intensity for each probe ? Using
 these command:
 library(aroma.affymetrix)
 cs - AffymetrixCelSet$byName(KN01M013, chipType=HG-U133_Plus_2)
 raw=extractMatrix(cs,verbose=verbose)
 
 I can see 'raw' is a list of intensities, but I don't know which probe
 ids they correspond to.  Hope this clarifies. Thanks
 
 On Aug 9, 6:03 am, Mark Robinson markrobinson@gmail.com wrote:
 Perhaps something like this is what you want (note: different chip to
 what you are using)?
 
 df - readDataFrame(getCdf(cs), verbose=-80)
 [...snip...]
 head(df)
  unit unitName   unitType unitDirection unitNbrOfAtoms group groupName
 11  7892501 expression sense  4 1
 7892501
 21  7892501 expression sense  4 1
 7892501
 31  7892501 expression sense  4 1
 7892501
 41  7892501 expression sense  4 1
 7892501
 52  7892502 expression sense  4 1
 7892502
 62  7892502 expression sense  4 1
 7892502
  groupDirection groupNbrOfAtomscell   x   y pbase tbase indexPos
 atom
 1  sense   4  116371 870 110 C G
 00
 2  sense   4  943979  28 899 A T
 11
 3  sense   4  493089 638 469 T A
 22
 4  sense   4  907039 888 863 A T
 33
 5  sense   4 1033309 108 984 T A
 00
 6  sense   4  653512 411 622 T A
 11
 
 I'm not sure what object you have in mind when it comes to a probe-
 intensity pair, but this should give you all the info you might want
 (e.g. cell index, x/y physical location).
 
 HTH,
 Mark
 
 On Aug 9, 5:45 pm, Pierre Neuvial pie...@stat.berkeley.edu wrote:
 
 Hi,
 
 Have you tried using extractAffyBatch, which is documented 
 here:http://aroma-project.org/howtos/extractAffyBatch?
 As far as I understand you will need the Bioconductor annotation
 package corresponding to your chip type to be installed, ie
 
  source(http://www.bioconductor.org/biocLite.R;)
  biocLite(hgu133plus2cdf)
 
 This is discussed in this 
 thread:http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/...
 
 Pierre
 
 On Tue, Aug 9, 2011 at 4:34 AM, hsingjun cheung
 
 hsingjun.ch...@gmail.com wrote:
 Hi Pierre:
 
 Thanks. These functions work now. Do you know how to extract the raw
 intensity for each probe ?
 
 On Aug 8, 5:48 pm, Pierre Neuvial pie...@stat.berkeley.edu wrote:
 Hi,
 
 The 'annotationData' directory should be directly in your working
 directory, as explained in the page Setup: Location of annotation
 data files:http://aroma-project.org/node/66
 
 In your case, you need to change the current directory to ~/experiment/ by
 
 setwd(~/experiment/)
 
 (or by starting your R session from this directory).  Then your command
 
 csR - AffymetrixCelSet$byName(KN01M013,chipType=HG-U133_Plus_2)
 
 should work.
 
 Best,
 
 Pierre
 
 On Mon, Aug 8, 2011 at 5:29 PM, hsingjun cheung
 
 hsingjun.ch...@gmail.com wrote:
 Hello:
 
 I searched the group but got no results ... So I want to know, how to
 extract the raw probe intensity from .CEL file?
 
 The file structure on my computer is like:
 
 ~/experiemnt/
 annotationData/
 chipTypes/
HG-U133_Plus_2/
   HG-U133_Plus_2.cdf
 ~/experiment/
   rawData/
   KN01M013/
   HG-U133_Plus_2/
KN01M013.CEL
 
 The .cdf file is downloaded 
 fromhttp://www.aroma-project.org/chipTypes/HG-U133_Plus_2
 
 When I run R under ~ directory:
 library(aroma.affymetrix)
  csR - AffymetrixCelSet$byName(KN01M013,chipType=HG-U133_Plus_2)
 
 I got error msg:
 
 Error in list(`AffymetrixCelSet$byName(KN01M013, chipType = HG-
 U133_Plus_2)` = environment,  :
 
 [2011-08-08 11:24:05] Exception: Could not locate a file for this chip
 type: HG-U133_Plus_2
  at throw(Exception(...))
  at throw.default(Could not locate a file for this chip type: ,
 paste(c(chipT
  at throw(Could not locate a file for this chip type: ,
 paste(c(chipType, tag
  at method(static, ...)
  at AffymetrixCdfFile$byChipType(chipType)
  at method(static, ...)
  at AffymetrixCelSet$byName(KN01M013, chipType = HG-U133_Plus_2)
 
 Could anyone help me figure how this error happened ? And how to do
 it  ( extract raw probe intensity ) in a right way ? Thanks
 
 --
 When reporting problems on aroma.affymetrix, make sure 1) to