Re: [aroma.affymetrix] Re: Failed to identify CDF unit with unit name

2012-11-19 Thread Raj Patrao 
Hello Henrik,

here is my script

basedir - Projects/DrugRep/GEOData/
srcdir = paste(basedir,AZD2,sep=)
workdir = paste(basedir,Workdir,sep=)
setwd(workdir)
tarFile-paste(basedir,AZD2/GSE4757_RAW.tar,sep=)
covdesc - paste(basedir,AZD2/GSE4757.covdesc,sep=)
 convertCdf(annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2.cdf,
annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2,bin.cdf)


gsedir- strsplit(basename(tarFile),'_')[[1]][1]

print(paste(Untarring,tarFile))
write(paste(Untarring,tarFile), file=test.log, append = TRUE)

 # create  a rawdata folder
# create annotationData Folder
dir.create(rawData,recursive=TRUE)
#dir.create(annotationData,recursive=TRUE)

# get annotation chip file if it does not exist in local folder
 
chipType - HG-U133_Plus_2
datafolder - paste(rawData/,gsedir,/,chipType,sep=)
dir.create(datafolder , recursive=TRUE)

untar(tarFile,exdir=datafolder)

 # Gunzip all the cel files
setwd(datafolder)
getwd()
celfiles - list.files(pattern=CEL.gz,ignore.case = TRUE)
lapply(celfiles,gunzip)

# Create Cdf object
setwd(../../..)
cdf - AffymetrixCdfFile$byChipType(chipType);
cs - AffymetrixCelSet$byName(gsedir, cdf=cdf);

# gcRMA background correction
bc - GcRmaBackgroundCorrection(cs);


#this is where it errors
##

csB - process(bc);

# RMA quantile normalization
qn - QuantileNormalization(csB, typesToUpdate=pm);
csN - process(qn);

# RMA probe summarization
plm - RmaPlm(csN, flavor=oligo);
fit(plm);

# Extract chip effects on the log2 scale
ces - getChipEffectSet(plm);
theta - extractMatrix(ces);
rownames(theta) - getUnitNames(cdf);
theta - log2(theta);



and here is my session info


   sessionInfo(); 
R version 2.15.0 (2012-03-30)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C  
[5] LC_TIME=English_United States.1252

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

other attached packages:
 [1] aroma.affymetrix_2.6.0 affxparser_1.30.0  aroma.apd_0.2.3   
 [4] R.huge_0.4.1   aroma.light_1.28.0 aroma.core_2.6.0  
 [7] matrixStats_0.5.3  R.rsp_0.8.2R.cache_0.6.3 
[10] R.devices_2.1.1R.filesets_1.1.5   digest_0.5.2  
[13] R.utils_1.18.0 R.oo_1.10.1R.methodsS3_1.4.2 
[16] e1071_1.6-1class_7.3-5   


thanks,
rajesh

On Monday, November 19, 2012 11:04:15 AM UTC+5:30, Henrik Bengtsson wrote:

 Hi, 

 I've never seen that before, but remove any *.tmp or *.tmp.tmp etc 
 files and try again.  If that does not work, then please 

 1. show your script exactly at it is, 

 2. show the output you get from 

   library(aroma.affymetrix); 
   sessionInfo(); 

 /Henrik. 

 On Sun, Nov 18, 2012 at 8:02 PM, Raj Patrao rlpa...@gmail.comjavascript: 
 wrote: 
  Thanks Much Henrik. 
  
  I used the ACS file, but I am not able to go further than the 
 process(). 
  I am getting an error 
  
  Error: Failed to rename temporary file: 
  probeData/GSE4757,OBC/HG-U133_Plus_2/GSM107523.CEL.tmp.tmp - 
  probeData/GSE4757,OBC/HG-U133_Plus_2/GSM107523.CEL.tmp 
  In addition: Warning messages: 
  1: In file.remove(pathnameT) : 
cannot remove file 'probeData/GSE4757,OBC/filef9050a139e3', reason 
  'Permission denied' 
  2: In file.remove(pathnameT) : 
cannot remove file 
 'probeData/GSE4757,OBC/HG-U133_Plus_2/filef90ba31c36', 
  reason 'Permission denied' 
  3: In file.remove(pathnameT) : 
cannot remove file 
 'probeData/GSE4757,OBC/HG-U133_Plus_2/filef909434baf', 
  reason 'Permission denied' 
  4: In file.remove(pathnameT) : 
cannot remove file 
 'probeData/GSE4757,OBC/HG-U133_Plus_2/filef90690e1d4d', 
  reason 'Permission denied' 
  
  
  Thanks, 
  Rajesh. 
  
  
  On Saturday, November 3, 2012 3:24:39 PM UTC+5:30, Raj Patrao wrote: 
  
  Hello All, 
  
  I am getting the following error when doing process in aroma: 
  
   csB - process(bc,verbose=TRUE); 
  Background correcting data set... 
   Computing probe affinities (independent of data)... 
  [2012-11-03 15:10:02] Exception: Failed to identify CDF unit with unit 
  name '1': annotationData/chipTypes/HG-U133_Plus_2/u133plus2gb_probe_tab 
  
at #09. getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, 
  verbose = verbose) 
- getProbeSequenceData.AffymetrixCdfFile() is in environment 
  'aroma.affymetrix' 
  
at #08. getProbeSequenceData(this, safe = safe, verbose = verbose) 
- getProbeSequenceData() is in environment 'aroma.affymetrix' 
  
at #07. computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, 
 ..., 
verbose = less(verbose)) 
- computeAffinities.AffymetrixCdfFile() is in environment 
  'aroma.affymetrix' 
  
at #06. computeAffinities(cdf, paths = probePath, ..., verbose =

Re: [aroma.affymetrix] Re: Failed to identify CDF unit with unit name

2012-11-19 Thread Henrik Bengtsson 
Did you retry by first remove any of those *.tmp or *.tmp.tmp etc and rerunning

dataSet - GSE4757,OBC;
chipType - HG-U133_Plus_2;
cdf - AffymetrixCdfFile$byChipType(chipType);
cs - AffymetrixCelSet$byName(dataSet, cdf=cdf);
print(cs);

bc - GcRmaBackgroundCorrection(cs);
print(bc);
csB - process(bc);
print(csB);

?

/Henrik

On Mon, Nov 19, 2012 at 1:27 AM, Raj Patrao rlpat...@gmail.com wrote:
 Hello Henrik,

 here is my script

 basedir - Projects/DrugRep/GEOData/
 srcdir = paste(basedir,AZD2,sep=)
 workdir = paste(basedir,Workdir,sep=)
 setwd(workdir)
 tarFile-paste(basedir,AZD2/GSE4757_RAW.tar,sep=)
 covdesc - paste(basedir,AZD2/GSE4757.covdesc,sep=)
 convertCdf(annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2.cdf,
 annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2,bin.cdf)


 gsedir- strsplit(basename(tarFile),'_')[[1]][1]

 print(paste(Untarring,tarFile))
 write(paste(Untarring,tarFile), file=test.log, append = TRUE)

 # create  a rawdata folder
 # create annotationData Folder
 dir.create(rawData,recursive=TRUE)
 #dir.create(annotationData,recursive=TRUE)

 # get annotation chip file if it does not exist in local folder

 chipType - HG-U133_Plus_2
 datafolder - paste(rawData/,gsedir,/,chipType,sep=)
 dir.create(datafolder , recursive=TRUE)

 untar(tarFile,exdir=datafolder)

 # Gunzip all the cel files
 setwd(datafolder)
 getwd()
 celfiles - list.files(pattern=CEL.gz,ignore.case = TRUE)
 lapply(celfiles,gunzip)

 # Create Cdf object
 setwd(../../..)
 cdf - AffymetrixCdfFile$byChipType(chipType);
 cs - AffymetrixCelSet$byName(gsedir, cdf=cdf);

 # gcRMA background correction
 bc - GcRmaBackgroundCorrection(cs);

 
 #this is where it errors
 ##

 csB - process(bc);

 # RMA quantile normalization
 qn - QuantileNormalization(csB, typesToUpdate=pm);
 csN - process(qn);

 # RMA probe summarization
 plm - RmaPlm(csN, flavor=oligo);
 fit(plm);

 # Extract chip effects on the log2 scale
 ces - getChipEffectSet(plm);
 theta - extractMatrix(ces);
 rownames(theta) - getUnitNames(cdf);
 theta - log2(theta);



 and here is my session info


   sessionInfo();
 R version 2.15.0 (2012-03-30)
 Platform: i386-pc-mingw32/i386 (32-bit)

 locale:
 [1] LC_COLLATE=English_United States.1252
 [2] LC_CTYPE=English_United States.1252
 [3] LC_MONETARY=English_United States.1252
 [4] LC_NUMERIC=C
 [5] LC_TIME=English_United States.1252

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

 other attached packages:
  [1] aroma.affymetrix_2.6.0 affxparser_1.30.0  aroma.apd_0.2.3
  [4] R.huge_0.4.1   aroma.light_1.28.0 aroma.core_2.6.0
  [7] matrixStats_0.5.3  R.rsp_0.8.2R.cache_0.6.3
 [10] R.devices_2.1.1R.filesets_1.1.5   digest_0.5.2
 [13] R.utils_1.18.0 R.oo_1.10.1R.methodsS3_1.4.2
 [16] e1071_1.6-1class_7.3-5


 thanks,
 rajesh

 On Monday, November 19, 2012 11:04:15 AM UTC+5:30, Henrik Bengtsson wrote:

 Hi,

 I've never seen that before, but remove any *.tmp or *.tmp.tmp etc
 files and try again.  If that does not work, then please

 1. show your script exactly at it is,

 2. show the output you get from

   library(aroma.affymetrix);
   sessionInfo();

 /Henrik.

 On Sun, Nov 18, 2012 at 8:02 PM, Raj Patrao rlpa...@gmail.com wrote:
  Thanks Much Henrik.
 
  I used the ACS file, but I am not able to go further than the
  process().
  I am getting an error
 
  Error: Failed to rename temporary file:
  probeData/GSE4757,OBC/HG-U133_Plus_2/GSM107523.CEL.tmp.tmp -
  probeData/GSE4757,OBC/HG-U133_Plus_2/GSM107523.CEL.tmp
  In addition: Warning messages:
  1: In file.remove(pathnameT) :
cannot remove file 'probeData/GSE4757,OBC/filef9050a139e3', reason
  'Permission denied'
  2: In file.remove(pathnameT) :
cannot remove file
  'probeData/GSE4757,OBC/HG-U133_Plus_2/filef90ba31c36',
  reason 'Permission denied'
  3: In file.remove(pathnameT) :
cannot remove file
  'probeData/GSE4757,OBC/HG-U133_Plus_2/filef909434baf',
  reason 'Permission denied'
  4: In file.remove(pathnameT) :
cannot remove file
  'probeData/GSE4757,OBC/HG-U133_Plus_2/filef90690e1d4d',
  reason 'Permission denied'
 
 
  Thanks,
  Rajesh.
 
 
  On Saturday, November 3, 2012 3:24:39 PM UTC+5:30, Raj Patrao wrote:
 
  Hello All,
 
  I am getting the following error when doing process in aroma:
 
   csB - process(bc,verbose=TRUE);
  Background correcting data set...
   Computing probe affinities (independent of data)...
  [2012-11-03 15:10:02] Exception: Failed to identify CDF unit with unit
  name '1': annotationData/chipTypes/HG-U133_Plus_2/u133plus2gb_probe_tab
 
at #09. getProbeSequenceData.AffymetrixCdfFile(this, safe = safe,
  verbose = verbose)
- getProbeSequenceData.AffymetrixCdfFile() is in environment
  'aroma.affymetrix'
 
at #08. getProbeSequenceData(this, safe = safe, verbose = verbose)
- getProbeSequenceData() is in environment

[aroma.affymetrix] Re: Failed to identify CDF unit with unit name

2012-11-19 Thread Raj Patrao 
Hentrik, 

I did delete all the files created and re-ran. I deleted complete folder 
structure below , as these files are created automatically .

*probeData*
* GSE4757,GRBC*
* GSE4757,OBC*


Also, I dont know on what basis these datasets are getting created (these 
are getting created in the process step), and if the OBC, GRBC annotations 
are same for all sets.As shown in my script :*  *

*for each of the series*  *{ *
* Untar it in a work dir*
* Gunzip all celfiles*
* set up cdf*
* set up cel file set*
* run background correction - here the probeData folder gets created*
*
*
*} *


I intend to process large number of series in a automated way, so I am 
trying these options.

Thanks,
Rajesh.
 
On Saturday, November 3, 2012 3:24:39 PM UTC+5:30, Raj Patrao wrote:

 *Hello All,*
 *
 *
 *I am getting the following error when doing process in aroma: *

  csB - process(bc,verbose=TRUE);
 Background correcting data set...
  Computing probe affinities (independent of data)...
 [2012-11-03 15:10:02] Exception: Failed to identify CDF unit with unit 
 name '1': annotationData/chipTypes/HG-U133_Plus_2/u133plus2gb_probe_tab

   at #09. getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, 
 verbose = verbose)
   - getProbeSequenceData.AffymetrixCdfFile() is in environment 
 'aroma.affymetrix'

   at #08. getProbeSequenceData(this, safe = safe, verbose = verbose)
   - getProbeSequenceData() is in environment 'aroma.affymetrix'

   at #07. computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., 
   verbose = less(verbose))
   - computeAffinities.AffymetrixCdfFile() is in environment 
 'aroma.affymetrix'

   at #06. computeAffinities(cdf, paths = probePath, ..., verbose = 
 less(verbose))
   - computeAffinities() is in environment 'aroma.affymetrix'

   at #05. bgAdjustGcrma.AffymetrixCelSet(structure(NA, .env = 
 environment, class = c(AffymetrixCelSet, 
   AffymetrixFileSet, AromaPlatformInterface, 
 AromaMicroarrayDataSet, 
   GenericDataFileSet, FullNameInterface, Object)), path = 
 probeData/GSE4757,GRBC/HG-U133_Plus_2, 
   verbose = structure(TRUE, .env = environment, class = 
 c(Verbose, 
   Object)), overwrite = FALSE, subsetToUpdate = NULL, 
 typesToUpdate = pm, 
   indicesNegativeControl = NULL, affinities = NULL, type = 
 fullmodel, 
   opticalAdjust = TRUE, gsbAdjust = TRUE, gsbParameters = 
 NULL, 
   .deprecated = FALSE)
   - bgAdjustGcrma.AffymetrixCelSet() is in environment 
 'aroma.affymetrix'

   at #04. bgAdjustGcrma(structure(NA, .env = environment, class = 
 c(AffymetrixCelSet, 
   AffymetrixFileSet, AromaPlatformInterface, 
 AromaMicroarrayDataSet, 
   GenericDataFileSet, FullNameInterface, Object)), path = 
 probeData/GSE4757,GRBC/HG-U133_Plus_2, 
   verbose = structure(TRUE, .env = environment, class = 
 c(Verbose, 
   Object)), overwrite = FALSE, subsetToUpdate = NULL, 
 typesToUpdate = pm, 
   indicesNegativeControl = NULL, affinities = NULL, type = 
 fullmodel, 
   opticalAdjust = TRUE, gsbAdjust = TRUE, gsbParameters = 
 NULL, 
   .deprecated = FALSE)
   - bgAdjustGcrma() is in environment 'aroma.affymetrix'

   at #03. do.call(bgAdjustGcrma, args = args)
   - do.call() is in environment 'base'

   at #02. process.GcRmaBackgroundCorrection(bc, verbose = TRUE)
   - process.GcRmaBackgroundCorrection() is in environment 
 'aroma.affymetrix'

   at #01. process(bc, verbose = TRUE)
   - process() is in environment 'aroma.core'

 Error: 
  Computing probe affinities (independent of data)...done
 Background correcting data set...done



 *Here is my directory structure : *

 annotationData
  

  annotationData\chipTypes\HG-U133_Plus_2

 11/03/2012  03:09 PMDIR  .
 11/03/2012  03:09 PMDIR  ..
 10/19/2012  10:49 AM99,044,850 HG-U133_Plus_2  - ascii.cdf
 10/26/2012  09:49 PM26,251,783 HG-U133_Plus_2.cdf
 10/29/2012  10:21 AM15,952,085 Hs133P_Hs_REFSEQ.cdf
 07/14/2005  12:23 AM23,991,168 u133plus2gb_probe_tab

   rawData\GSE4757\HG-U133_Plus_2

 10/26/2012  09:18 PMDIR  .
 10/26/2012  09:18 PMDIR  ..
 10/26/2012  09:17 PM13,555,389 GSM107522.cel
 10/26/2012  09:17 PM13,556,785 GSM107523.cel
 10/26/2012  09:17 PM13,560,384 GSM107524.cel
 10/26/2012  09:17 PM13,556,716 GSM107525.cel
 10/26/2012  09:17 PM13,552,046 GSM107526.cel
 10/26/2012  09:17 PM13,552,689 GSM107527.cel
 10/26/2012  09:17 PM13,553,222 GSM107528.cel
 10/26/2012  09:17 PM13,552,445 GSM107529.cel
 10/26/2012  09:17 PM13,551,059 GSM107530.cel
 10/26/2012  09:17 PM13,550,482 GSM107531.cel
 10/26/2012  09:17 PM13,550,367 GSM107532.cel
 10/26/2012  09:17 PM13,550,546

[aroma.affymetrix] Re: Failed to identify CDF unit with unit name

2012-11-18 Thread Raj Patrao 
Thanks Much Henrik.

I used the ACS file, but I am not able to go further than the process(). 
 I am getting an error 

Error: Failed to rename temporary file: 
probeData/GSE4757,OBC/HG-U133_Plus_2/GSM107523.CEL.tmp.tmp - 
probeData/GSE4757,OBC/HG-U133_Plus_2/GSM107523.CEL.tmp
In addition: Warning messages:
1: In file.remove(pathnameT) :
  cannot remove file 'probeData/GSE4757,OBC/filef9050a139e3', reason 
'Permission denied'
2: In file.remove(pathnameT) :
  cannot remove file 'probeData/GSE4757,OBC/HG-U133_Plus_2/filef90ba31c36', 
reason 'Permission denied'
3: In file.remove(pathnameT) :
  cannot remove file 'probeData/GSE4757,OBC/HG-U133_Plus_2/filef909434baf', 
reason 'Permission denied'
4: In file.remove(pathnameT) :
  cannot remove file 
'probeData/GSE4757,OBC/HG-U133_Plus_2/filef90690e1d4d', reason 'Permission 
denied'


Thanks,
Rajesh.

On Saturday, November 3, 2012 3:24:39 PM UTC+5:30, Raj Patrao wrote:

 *Hello All,*
 *
 *
 *I am getting the following error when doing process in aroma: *

  csB - process(bc,verbose=TRUE);
 Background correcting data set...
  Computing probe affinities (independent of data)...
 [2012-11-03 15:10:02] Exception: Failed to identify CDF unit with unit 
 name '1': annotationData/chipTypes/HG-U133_Plus_2/u133plus2gb_probe_tab

   at #09. getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, 
 verbose = verbose)
   - getProbeSequenceData.AffymetrixCdfFile() is in environment 
 'aroma.affymetrix'

   at #08. getProbeSequenceData(this, safe = safe, verbose = verbose)
   - getProbeSequenceData() is in environment 'aroma.affymetrix'

   at #07. computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., 
   verbose = less(verbose))
   - computeAffinities.AffymetrixCdfFile() is in environment 
 'aroma.affymetrix'

   at #06. computeAffinities(cdf, paths = probePath, ..., verbose = 
 less(verbose))
   - computeAffinities() is in environment 'aroma.affymetrix'

   at #05. bgAdjustGcrma.AffymetrixCelSet(structure(NA, .env = 
 environment, class = c(AffymetrixCelSet, 
   AffymetrixFileSet, AromaPlatformInterface, 
 AromaMicroarrayDataSet, 
   GenericDataFileSet, FullNameInterface, Object)), path = 
 probeData/GSE4757,GRBC/HG-U133_Plus_2, 
   verbose = structure(TRUE, .env = environment, class = 
 c(Verbose, 
   Object)), overwrite = FALSE, subsetToUpdate = NULL, 
 typesToUpdate = pm, 
   indicesNegativeControl = NULL, affinities = NULL, type = 
 fullmodel, 
   opticalAdjust = TRUE, gsbAdjust = TRUE, gsbParameters = 
 NULL, 
   .deprecated = FALSE)
   - bgAdjustGcrma.AffymetrixCelSet() is in environment 
 'aroma.affymetrix'

   at #04. bgAdjustGcrma(structure(NA, .env = environment, class = 
 c(AffymetrixCelSet, 
   AffymetrixFileSet, AromaPlatformInterface, 
 AromaMicroarrayDataSet, 
   GenericDataFileSet, FullNameInterface, Object)), path = 
 probeData/GSE4757,GRBC/HG-U133_Plus_2, 
   verbose = structure(TRUE, .env = environment, class = 
 c(Verbose, 
   Object)), overwrite = FALSE, subsetToUpdate = NULL, 
 typesToUpdate = pm, 
   indicesNegativeControl = NULL, affinities = NULL, type = 
 fullmodel, 
   opticalAdjust = TRUE, gsbAdjust = TRUE, gsbParameters = 
 NULL, 
   .deprecated = FALSE)
   - bgAdjustGcrma() is in environment 'aroma.affymetrix'

   at #03. do.call(bgAdjustGcrma, args = args)
   - do.call() is in environment 'base'

   at #02. process.GcRmaBackgroundCorrection(bc, verbose = TRUE)
   - process.GcRmaBackgroundCorrection() is in environment 
 'aroma.affymetrix'

   at #01. process(bc, verbose = TRUE)
   - process() is in environment 'aroma.core'

 Error: 
  Computing probe affinities (independent of data)...done
 Background correcting data set...done



 *Here is my directory structure : *

 annotationData
  

  annotationData\chipTypes\HG-U133_Plus_2

 11/03/2012  03:09 PMDIR  .
 11/03/2012  03:09 PMDIR  ..
 10/19/2012  10:49 AM99,044,850 HG-U133_Plus_2  - ascii.cdf
 10/26/2012  09:49 PM26,251,783 HG-U133_Plus_2.cdf
 10/29/2012  10:21 AM15,952,085 Hs133P_Hs_REFSEQ.cdf
 07/14/2005  12:23 AM23,991,168 u133plus2gb_probe_tab

   rawData\GSE4757\HG-U133_Plus_2

 10/26/2012  09:18 PMDIR  .
 10/26/2012  09:18 PMDIR  ..
 10/26/2012  09:17 PM13,555,389 GSM107522.cel
 10/26/2012  09:17 PM13,556,785 GSM107523.cel
 10/26/2012  09:17 PM13,560,384 GSM107524.cel
 10/26/2012  09:17 PM13,556,716 GSM107525.cel
 10/26/2012  09:17 PM13,552,046 GSM107526.cel
 10/26/2012  09:17 PM13,552,689 GSM107527.cel
 10/26/2012  09:17 PM13,553,222 GSM107528.cel
 10/26/2012  09:17 PM13,552,445 GSM107529.cel
 10/26/2012  09:17 PM13,551,059 GSM107530.cel
 10/26/2012  09:17 PM13,550,482

Re: [aroma.affymetrix] Re: Failed to identify CDF unit with unit name

2012-11-18 Thread Henrik Bengtsson 
Hi,

I've never seen that before, but remove any *.tmp or *.tmp.tmp etc
files and try again.  If that does not work, then please

1. show your script exactly at it is,

2. show the output you get from

  library(aroma.affymetrix);
  sessionInfo();

/Henrik.

On Sun, Nov 18, 2012 at 8:02 PM, Raj Patrao rlpat...@gmail.com wrote:
 Thanks Much Henrik.

 I used the ACS file, but I am not able to go further than the process().
 I am getting an error

 Error: Failed to rename temporary file:
 probeData/GSE4757,OBC/HG-U133_Plus_2/GSM107523.CEL.tmp.tmp -
 probeData/GSE4757,OBC/HG-U133_Plus_2/GSM107523.CEL.tmp
 In addition: Warning messages:
 1: In file.remove(pathnameT) :
   cannot remove file 'probeData/GSE4757,OBC/filef9050a139e3', reason
 'Permission denied'
 2: In file.remove(pathnameT) :
   cannot remove file 'probeData/GSE4757,OBC/HG-U133_Plus_2/filef90ba31c36',
 reason 'Permission denied'
 3: In file.remove(pathnameT) :
   cannot remove file 'probeData/GSE4757,OBC/HG-U133_Plus_2/filef909434baf',
 reason 'Permission denied'
 4: In file.remove(pathnameT) :
   cannot remove file 'probeData/GSE4757,OBC/HG-U133_Plus_2/filef90690e1d4d',
 reason 'Permission denied'


 Thanks,
 Rajesh.


 On Saturday, November 3, 2012 3:24:39 PM UTC+5:30, Raj Patrao wrote:

 Hello All,

 I am getting the following error when doing process in aroma:

  csB - process(bc,verbose=TRUE);
 Background correcting data set...
  Computing probe affinities (independent of data)...
 [2012-11-03 15:10:02] Exception: Failed to identify CDF unit with unit
 name '1': annotationData/chipTypes/HG-U133_Plus_2/u133plus2gb_probe_tab

   at #09. getProbeSequenceData.AffymetrixCdfFile(this, safe = safe,
 verbose = verbose)
   - getProbeSequenceData.AffymetrixCdfFile() is in environment
 'aroma.affymetrix'

   at #08. getProbeSequenceData(this, safe = safe, verbose = verbose)
   - getProbeSequenceData() is in environment 'aroma.affymetrix'

   at #07. computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ...,
   verbose = less(verbose))
   - computeAffinities.AffymetrixCdfFile() is in environment
 'aroma.affymetrix'

   at #06. computeAffinities(cdf, paths = probePath, ..., verbose =
 less(verbose))
   - computeAffinities() is in environment 'aroma.affymetrix'

   at #05. bgAdjustGcrma.AffymetrixCelSet(structure(NA, .env =
 environment, class = c(AffymetrixCelSet,
   AffymetrixFileSet, AromaPlatformInterface,
 AromaMicroarrayDataSet,
   GenericDataFileSet, FullNameInterface, Object)), path =
 probeData/GSE4757,GRBC/HG-U133_Plus_2,
   verbose = structure(TRUE, .env = environment, class =
 c(Verbose,
   Object)), overwrite = FALSE, subsetToUpdate = NULL,
 typesToUpdate = pm,
   indicesNegativeControl = NULL, affinities = NULL, type =
 fullmodel,
   opticalAdjust = TRUE, gsbAdjust = TRUE, gsbParameters =
 NULL,
   .deprecated = FALSE)
   - bgAdjustGcrma.AffymetrixCelSet() is in environment
 'aroma.affymetrix'

   at #04. bgAdjustGcrma(structure(NA, .env = environment, class =
 c(AffymetrixCelSet,
   AffymetrixFileSet, AromaPlatformInterface,
 AromaMicroarrayDataSet,
   GenericDataFileSet, FullNameInterface, Object)), path =
 probeData/GSE4757,GRBC/HG-U133_Plus_2,
   verbose = structure(TRUE, .env = environment, class =
 c(Verbose,
   Object)), overwrite = FALSE, subsetToUpdate = NULL,
 typesToUpdate = pm,
   indicesNegativeControl = NULL, affinities = NULL, type =
 fullmodel,
   opticalAdjust = TRUE, gsbAdjust = TRUE, gsbParameters =
 NULL,
   .deprecated = FALSE)
   - bgAdjustGcrma() is in environment 'aroma.affymetrix'

   at #03. do.call(bgAdjustGcrma, args = args)
   - do.call() is in environment 'base'

   at #02. process.GcRmaBackgroundCorrection(bc, verbose = TRUE)
   - process.GcRmaBackgroundCorrection() is in environment
 'aroma.affymetrix'

   at #01. process(bc, verbose = TRUE)
   - process() is in environment 'aroma.core'

 Error:
  Computing probe affinities (independent of data)...done
 Background correcting data set...done



 Here is my directory structure :

 annotationData


  annotationData\chipTypes\HG-U133_Plus_2

 11/03/2012  03:09 PMDIR  .
 11/03/2012  03:09 PMDIR  ..
 10/19/2012  10:49 AM99,044,850 HG-U133_Plus_2  - ascii.cdf
 10/26/2012  09:49 PM26,251,783 HG-U133_Plus_2.cdf
 10/29/2012  10:21 AM15,952,085 Hs133P_Hs_REFSEQ.cdf
 07/14/2005  12:23 AM23,991,168 u133plus2gb_probe_tab

   rawData\GSE4757\HG-U133_Plus_2

 10/26/2012  09:18 PMDIR  .
 10/26/2012  09:18 PMDIR  ..
 10/26/2012  09:17 PM13,555,389 GSM107522.cel
 10/26/2012  09:17 PM13,556,785 GSM107523.cel
 10/26/2012  09:17 PM13,560,384 GSM107524.cel
 10/26/2012  09:17 PM13,556,716 GSM107525.cel
 10/26/2012  09:17