Re: [aroma.affymetrix] Problem in indexof with version aroma.affymetrix 2.1.0

2011-06-07 Thread Henrik Bengtsson
Hi,

first of all, indexOf(cdf, pattern=) does indeed work, e.g.

 cdf - AffymetrixCdfFile$byChipType(Mapping10K_Xba142);
 units - indexOf(cdf, pattern=);
 str(units)
 int [1:10208] 1 2 3 4 5 6 7 8 9 10 ...

Your 'cdfT' object seems not to be what you think it is, i.e. it is
not an AffymetrixCdfFile object.  It seems to be a simple string
(character).

I don't think your problem is related to updates in aroma.affymetrix.
However, the underlying error may be caught earlier now, so you end up
getting a different error.

Also, I don't know what the SPACE script / ComputeGmatrix comes from
- is that something you wrote or someone else?  If someone else, wrote
it, have you checked with that person?

Cheers,

Henrik


On Mon, May 30, 2011 at 2:24 AM, Ravi Sharma rdsharm...@gmail.com wrote:

 Hello,

 #

 Here is the session Information:

sessionInfo()

 R version 2.12.1 (2010-12-16)

 Platform: x86_64-redhat-linux-gnu (64-bit)

 locale:
  [1] LC_CTYPE=en_US.utf8   LC_NUMERIC=C
  [3] LC_TIME=en_US.utf8    LC_COLLATE=en_US.utf8
  [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8
  [7] LC_PAPER=en_US.utf8   LC_NAME=C
  [9] LC_ADDRESS=C  LC_TELEPHONE=C
 [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

 attached base packages:
 [1] stats graphics  grDevices utils datasets  methods   base

 other attached packages:
  [1] SPACE_1.0  combinat_0.0-8 graph_1.28.0
  [4] MASS_7.3-9 aroma.affymetrix_2.1.1 aroma.apd_0.1.8
  [7] affxparser_1.22.1  R.huge_0.2.2   aroma.core_2.1.1
 [10] aroma.light_1.18.4 matrixStats_0.2.2  R.rsp_0.5.4
 [13] R.cache_0.4.2  R.filesets_1.0.2   digest_0.4.2
 [16] R.utils_1.7.6  R.oo_1.8.0 R.methodsS3_1.2.1

 loaded via a namespace (and not attached):
 [1] tools_2.12.1

 #

 I was running the SPACE script (ComputeGmatrix) to generate G and GE
 matrices with aroma.affymetrix_2.1.1. I got the following error:

Glist-ComputeGmatrix(cdfG,cdfT)

 Reading indexes for genes...done

 Reading indexes for units (units(G)=transcripts units(GE)=exons)...Error in
 UseMethod(indexOf) :

 no applicable method for 'indexOf' applied to an object of class character

 #

 Than, i run the source code of ComputeGmatrix (Source code is attached with
 mail) and i got the following error.

unitsT - indexOf(cdfT, pattern='')

 Error in UseMethod(indexOf) :

 no applicable method for 'indexOf' applied to an object of class character

 #

 However, in case of cdfG it is working:

 unitsG - indexOf(cdfG, pattern='')

 #

 'CDFs' information are given here:

 cdfG

 AffymetrixCdfFile:

 Path: annotationData/chipTypes/hjay

 Filename: hjay,r1.cdf

 Filesize: 107.39MB

 Chip type: hjay,r1

 RAM: 1.81MB

 File format: v4 (binary; XDA)

 Dimension: 2560x2560

 Number of cells: 6553600

 Number of units: 33845

 Cells per unit: 193.64

 Number of QC units: 0

 cdfT

 AffymetrixCdfFile:

 Path: annotationData/chipTypes/hjay

 Filename: hjay,r1,tr,9.cdf

 Filesize: 233.38MB

 Chip type: hjay,r1,tr,9

 RAM: 0.00MB

 File format: v4 (binary; XDA)

 Dimension: 2560x2560

 Number of cells: 6553600

 Number of units: 83374

 Cells per unit: 78.60

 Number of QC units: 0

 #

 With previously version of aroma.affymetrix i was getting the wrong indices
 in script ComputeGmatrix (a small part of script is below)

 patternT=''

cat(Reading indexes for units (units(G)=transcripts units(GE)=exons)...);

unitsT - indexOf.UnitNamesFile(cdfT, pattern=patternT)

transcripts - getUnitNames(cdfT, units=unitsT)

indicesT - getCellIndices(cdfT,units=unitsT)

 so i updated the version of aroma.affyemtrix, and now i am not able to get
 even units name for cdfT.

 regards,

 Ravi


 On Fri, May 27, 2011 at 8:20 PM, Henrik Bengtsson
 henrik.bengts...@aroma-project.org wrote:

 Hi,

 please provide you full script showing what you are trying to do and
 where you get errors.  Don't forget to also report your sessionInfo().
  Please all give the full details of the CDFs you are referring to.

 /Henrik

 On Fri, May 27, 2011 at 4:22 AM, Ravi Sharma rdsharm...@gmail.com wrote:
 
  Dear,
 
  Let me describe from beginning, I was facing the problem of  wrong cell
  indeces using 'getCellIndices' command (with an older version of
  aroma.affymetrix) but i was able to retrieve the indeces. After some
  search,
  i found that new version of aroma.affymetrix 2.1.0 perhaps 2.0.6 has
  resolved this problem. So i have updated the aroma.affymetrix version.
  Now i can' not even retrieve the index of Units using indexof commnand
  the
  error message is :
 
  no applicable method for 'indexOf' applied to an object of class
  character
 
  Probably that correspond to the CDF file:
  I am using 3 CDFs:
   For 1) Gene  2) Transcript  3) exons
 
  I tried indexof command with gene CDF and its working because
  (probably)
  Units are in numeric format,  However, failed with concern of transcript
  and
  Exon CDFs probably 'alpha numeric' format of Units.
 

Re: [aroma.affymetrix] Problem in indexof with version aroma.affymetrix 2.1.0

2011-05-30 Thread Ravi Sharma
Hello,

 #

Here is the session Information:

sessionInfo()

R version 2.12.1 (2010-12-16)

Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.utf8   LC_NUMERIC=C
 [3] LC_TIME=en_US.utf8LC_COLLATE=en_US.utf8
 [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8
 [7] LC_PAPER=en_US.utf8   LC_NAME=C
 [9] LC_ADDRESS=C  LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

other attached packages:
 [1] SPACE_1.0  combinat_0.0-8 graph_1.28.0
 [4] MASS_7.3-9 aroma.affymetrix_2.1.1 aroma.apd_0.1.8
 [7] affxparser_1.22.1  R.huge_0.2.2   aroma.core_2.1.1
[10] aroma.light_1.18.4 matrixStats_0.2.2  R.rsp_0.5.4
[13] R.cache_0.4.2  R.filesets_1.0.2   digest_0.4.2
[16] R.utils_1.7.6  R.oo_1.8.0 R.methodsS3_1.2.1

loaded via a namespace (and not attached):
[1] tools_2.12.1


#

I was running the SPACE script (ComputeGmatrix) to generate G and GE
matrices with aroma.affymetrix_2.1.1. I got the following error:

Glist-ComputeGmatrix(cdfG,cdfT)

Reading indexes for genes...done

Reading indexes for units (units(G)=transcripts units(GE)=exons)...Error in
UseMethod(indexOf) :

no applicable method for 'indexOf' applied to an object of class character



 #

Than, i run the source code of ComputeGmatrix (Source code is attached with
mail) and i got the following error.

 unitsT - indexOf(cdfT, pattern='')

Error in UseMethod(indexOf) :

no applicable method for 'indexOf' applied to an object of class character



#

However, in case of cdfG it is working:

 unitsG - indexOf(cdfG, pattern='')


#

'CDFs' information are given here:

 cdfG

AffymetrixCdfFile:

Path: annotationData/chipTypes/hjay

Filename: hjay,r1.cdf

Filesize: 107.39MB

Chip type: hjay,r1

RAM: 1.81MB

File format: v4 (binary; XDA)

Dimension: 2560x2560

Number of cells: 6553600

Number of units: 33845

Cells per unit: 193.64

Number of QC units: 0


  cdfT

AffymetrixCdfFile:

Path: annotationData/chipTypes/hjay

Filename: hjay,r1,tr,9.cdf

Filesize: 233.38MB

Chip type: hjay,r1,tr,9

RAM: 0.00MB

File format: v4 (binary; XDA)

Dimension: 2560x2560

Number of cells: 6553600

Number of units: 83374

Cells per unit: 78.60

Number of QC units: 0


#

With previously version of aroma.affymetrix i was getting the wrong indices
in script ComputeGmatrix (a small part of script is below)

 patternT=''

cat(Reading indexes for units (units(G)=transcripts units(GE)=exons)...);

unitsT - indexOf.UnitNamesFile(cdfT, pattern=patternT)

transcripts - getUnitNames(cdfT, units=unitsT)

indicesT - getCellIndices(cdfT,units=unitsT)


 so i updated the version of aroma.affyemtrix, and now i am not able to get
even units name for cdfT.


regards,

Ravi



On Fri, May 27, 2011 at 8:20 PM, Henrik Bengtsson 
henrik.bengts...@aroma-project.org wrote:

 Hi,

 please provide you full script showing what you are trying to do and
 where you get errors.  Don't forget to also report your sessionInfo().
  Please all give the full details of the CDFs you are referring to.

 /Henrik

 On Fri, May 27, 2011 at 4:22 AM, Ravi Sharma rdsharm...@gmail.com wrote:
 
  Dear,
 
  Let me describe from beginning, I was facing the problem of  wrong cell
  indeces using 'getCellIndices' command (with an older version of
  aroma.affymetrix) but i was able to retrieve the indeces. After some
 search,
  i found that new version of aroma.affymetrix 2.1.0 perhaps 2.0.6 has
  resolved this problem. So i have updated the aroma.affymetrix version.
  Now i can' not even retrieve the index of Units using indexof commnand
 the
  error message is :
 
  no applicable method for 'indexOf' applied to an object of class
 character
 
  Probably that correspond to the CDF file:
  I am using 3 CDFs:
   For 1) Gene  2) Transcript  3) exons
 
  I tried indexof command with gene CDF and its working because
 (probably)
  Units are in numeric format,  However, failed with concern of transcript
 and
  Exon CDFs probably 'alpha numeric' format of Units.
 
  any possible suggestion?
 
 
 
  regards,
  Ravi
 
 
  --
  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.


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