subject:"Re\: \[aroma.affymetrix\] \[A problem on fitting a log additive probe level model \(PLM\)"

Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)

2014-09-17 Thread Henrik Bengtsson

(Back to the public forum)

REPRODUCIBLE EXAMPLE:
It's a bug (still to be found) that shows itself when one runs the
analysis in one directory up from the root /, e.g. /arom-anal/.  I
managed to reproduce this by running a standard analysis in /tmp/.

WORKAROUND:
Run the analysis in directory that is at least one step deeper, e.g.
/foo/arom-anal/.  The problem goes away when I run the analysis in
/tmp/foo/.

Please confirm that the above workaround also works for you and thanks
for reporting on this.  I'll fix the bug as soon as I can.

/Henrik

On Tue, Sep 16, 2014 at 10:52 PM, jjspring OH sshshoh1...@gmail.com wrote:


 yes it is working

 Arguments$getReadablePath(plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1)
 [1] plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1


 Sunghee











 Sunghee Oh, PhD
 Director, Kim Sook Za Children's Hospital Medical Center Research
 Foundation,
 745 JikJi Daero Heung Deok Gu
 Cheng Ju City Chung Buk
 361-841, S. Korea








 On Wed, Sep 17, 2014 at 2:48 PM, Henrik Bengtsson h...@biostat.ucsf.edu
 wrote:

 Let's continue this off the list to spare the others the noise and
 post back when we found the solution.

 Continuing, and before I'll have to dig into the low-level code to
 figure out why you possibly could get this weird problem, does

 Arguments$getReadablePath(plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1)

 work as well?

 /Henrik



 On Tue, Sep 16, 2014 at 10:40 PM, jjspring OH sshshoh1...@gmail.com
 wrote:
 
 
 
  Hi Henrik,
 
  See the outputs:
 
  path - getPath(plm)
  print(path)
  [1] plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1
  dir(plmData)
  [1] tissues,RBC,QN,RMAtissues,RBC,QN,RMA,merged
  isDirectory(plmData)
  [1] TRUE
  Arguments$getReadablePath(plmData)
  [1] plmData
 
 
 
 
 
 
 
 
 
 
 
 
  2014년 9월 17일 수요일 오후 2시 14분 45초 UTC+9, Henrik Bengtsson 님의 말:
 
  Ok, and then the output of:
 
  path - getPath(plm)
  print(path)
  dir(plmData)
  isDirectory(plmData)
  Arguments$getReadablePath(plmData)
 
  /H
 
 
  On Tue, Sep 16, 2014 at 9:57 PM, jjspring OH sshsh...@gmail.com
  wrote:
   Hi Henrik,
  
   See below:
  
  
   print(plm)
   RmaPlm:
   Data set: tissues
   Chip type: RaGene-1_0-st-v1,r3
   Input tags: RBC,QN
   Output tags: RBC,QN,RMA
   Parameters: {probeModel: chr pm, shift: num 0, flavor: chr
   affyPLM,
   treatNAsAs: chr weights}
   Path: plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1
   RAM: 0.00MB
   print(getwd())
   [1] /arom-anal
  
  
   Thanks
   Sunghee
  
  
   2014년 9월 17일 수요일 오후 1시 45분 53초 UTC+9, Henrik Bengtsson 님의 말:
  
   That is really odd and I've never seen that error (8-9 years now).
   There must be a simple answer to this.  What does:
  
   print(plm)
   print(getwd())
  
   output when you get to that step.
  
   /Henrik
  
  
   On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH sshsh...@gmail.com
   wrote:
   
   
Hi,
   
After setting up the directory, performed background correction
and
rank
based quantile normalization,
   
   
   
library(aroma.affymetrix)
   
verbose - Arguments$getVerbose(-8, timestamp=T)
   
chipType - RaGene-1_0-st-v1
   
cdf - AffymetrixCdfFile$byChipType(chipType, tags=r3)
   
cs - AffymetrixCelSet$byName(tissues,cdf=cdf)
   
   
print(cs)
   
   
cs
AffymetrixCelSet:
Name: tissues
Tags:
Path: ../../arom-anal/rawData/tissues/RaGene-1_0-st-v1
Platform: Affymetrix
Chip type: RaGene-1_0-st-v1,r3
Number of arrays: 8
Names: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1), CS
_
7_(RaGene-1_0-st-v1), ..., NS _ 5_(RaGene-1_0-st-v1) [8]
Time period: 2012-06-02 14:22:20 -- 2012-06-02 16:29:33
Total file size: 84.50MB
RAM: 0.01MB
   
   
bc - RmaBackgroundCorrection(cs)
   
csBC - process(bc,verbose=verbose)
   
   
   
qn - QuantileNormalization(csBC, typesToUpdate = pm)
   
print(qn)
   
csN  - process(qn, verbose = verbose)
   
plm - RmaPlm(csN)
   
print(plm)
   
   
   
Until here, looks fine, BUT, when i perform fit function as below
and
the
errors come out related with directory,
   
fit(plm, verbose = verbose)
   
qam - QualityAssessmentModel(plm)
   
#plotNuse(qam)
   
plotRle(qam)
   
   
   
current directory is /arom-anal, and setting up the data files
(annotation,
cel files, and raw data) look fine(see below hierarchical
structure
of
directories),
After you take a closer look at the following errors, could you
please
let
me know what the problems are?
   
   
   
Creating CEL file...done
[2014-09-17 13:29:59] Exception: Pathname not found:
   
   
   
arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/probeAffinities.CEL
(none of the parent directories
[arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/] exist;
current
directory is '/arom-anal')
   
  at #22. getReadablePathname.Arguments(static, ...)
  - getReadablePathname.Arguments()

Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)

2014-09-17 Thread Henrik Bengtsson

I've narrowed down this bug to the R.utils package and fixed it.  I've
verified that the RMA pipeline now also works running in /tmp/.
Update aroma.affymetrix (including R.utils) by running:

source(http://callr.org/install#aroma.affymetrix;)

in a fresh R session.

/Henrik


On Tue, Sep 16, 2014 at 11:11 PM, jjspring OH sshshoh1...@gmail.com wrote:
 Finally working well after changing into one step further deeper directory
 as your comment,

 Sunghee


 2014년 9월 17일 수요일 오후 3시 2분 20초 UTC+9, Henrik Bengtsson 님의 말:

 (Back to the public forum)

 REPRODUCIBLE EXAMPLE:
 It's a bug (still to be found) that shows itself when one runs the
 analysis in one directory up from the root /, e.g. /arom-anal/.  I
 managed to reproduce this by running a standard analysis in /tmp/.

 WORKAROUND:
 Run the analysis in directory that is at least one step deeper, e.g.
 /foo/arom-anal/.  The problem goes away when I run the analysis in
 /tmp/foo/.

 Please confirm that the above workaround also works for you and thanks
 for reporting on this.  I'll fix the bug as soon as I can.

 /Henrik

 On Tue, Sep 16, 2014 at 10:52 PM, jjspring OH sshsh...@gmail.com wrote:
 
 
  yes it is working
 
 
  Arguments$getReadablePath(plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1)
  [1] plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1
 
 
  Sunghee
 
 
 
 
 
 
 
 
 
 
 
  Sunghee Oh, PhD
  Director, Kim Sook Za Children's Hospital Medical Center Research
  Foundation,
  745 JikJi Daero Heung Deok Gu
  Cheng Ju City Chung Buk
  361-841, S. Korea
 
 
 
 
 
 
 
 
  On Wed, Sep 17, 2014 at 2:48 PM, Henrik Bengtsson
  h...@biostat.ucsf.edu
  wrote:
 
  Let's continue this off the list to spare the others the noise and
  post back when we found the solution.
 
  Continuing, and before I'll have to dig into the low-level code to
  figure out why you possibly could get this weird problem, does
 
 
  Arguments$getReadablePath(plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1)
 
  work as well?
 
  /Henrik
 
 
 
  On Tue, Sep 16, 2014 at 10:40 PM, jjspring OH sshsh...@gmail.com
  wrote:
  
  
  
   Hi Henrik,
  
   See the outputs:
  
   path - getPath(plm)
   print(path)
   [1] plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1
   dir(plmData)
   [1] tissues,RBC,QN,RMAtissues,RBC,QN,RMA,merged
   isDirectory(plmData)
   [1] TRUE
   Arguments$getReadablePath(plmData)
   [1] plmData
  
  
  
  
  
  
  
  
  
  
  
  
   2014년 9월 17일 수요일 오후 2시 14분 45초 UTC+9, Henrik Bengtsson 님의 말:
  
   Ok, and then the output of:
  
   path - getPath(plm)
   print(path)
   dir(plmData)
   isDirectory(plmData)
   Arguments$getReadablePath(plmData)
  
   /H
  
  
   On Tue, Sep 16, 2014 at 9:57 PM, jjspring OH sshsh...@gmail.com
   wrote:
Hi Henrik,
   
See below:
   
   
print(plm)
RmaPlm:
Data set: tissues
Chip type: RaGene-1_0-st-v1,r3
Input tags: RBC,QN
Output tags: RBC,QN,RMA
Parameters: {probeModel: chr pm, shift: num 0, flavor: chr
affyPLM,
treatNAsAs: chr weights}
Path: plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1
RAM: 0.00MB
print(getwd())
[1] /arom-anal
   
   
Thanks
Sunghee
   
   
2014년 9월 17일 수요일 오후 1시 45분 53초 UTC+9, Henrik Bengtsson 님의 말:
   
That is really odd and I've never seen that error (8-9 years
now).
There must be a simple answer to this.  What does:
   
print(plm)
print(getwd())
   
output when you get to that step.
   
/Henrik
   
   
On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH sshsh...@gmail.com
wrote:


 Hi,

 After setting up the directory, performed background correction
 and
 rank
 based quantile normalization,



 library(aroma.affymetrix)

 verbose - Arguments$getVerbose(-8, timestamp=T)

 chipType - RaGene-1_0-st-v1

 cdf - AffymetrixCdfFile$byChipType(chipType, tags=r3)

 cs - AffymetrixCelSet$byName(tissues,cdf=cdf)


 print(cs)


 cs
 AffymetrixCelSet:
 Name: tissues
 Tags:
 Path: ../../arom-anal/rawData/tissues/RaGene-1_0-st-v1
 Platform: Affymetrix
 Chip type: RaGene-1_0-st-v1,r3
 Number of arrays: 8
 Names: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1),
 CS
 _
 7_(RaGene-1_0-st-v1), ..., NS _ 5_(RaGene-1_0-st-v1) [8]
 Time period: 2012-06-02 14:22:20 -- 2012-06-02 16:29:33
 Total file size: 84.50MB
 RAM: 0.01MB


 bc - RmaBackgroundCorrection(cs)

 csBC - process(bc,verbose=verbose)



 qn - QuantileNormalization(csBC, typesToUpdate = pm)

 print(qn)

 csN  - process(qn, verbose = verbose)

 plm - RmaPlm(csN)

 print(plm)



 Until here, looks fine, BUT, when i perform fit function as
 below
 and
 the
 errors come out related with directory,

 fit(plm, verbose = verbose)

 qam - QualityAssessmentModel(plm)

 #plotNuse(qam)

 plotRle(qam)

Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)

2014-09-16 Thread Henrik Bengtsson

That is really odd and I've never seen that error (8-9 years now).
There must be a simple answer to this.  What does:

print(plm)
print(getwd())

output when you get to that step.

/Henrik


On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH sshshoh1...@gmail.com wrote:


 Hi,

 After setting up the directory, performed background correction and rank
 based quantile normalization,



 library(aroma.affymetrix)

 verbose - Arguments$getVerbose(-8, timestamp=T)

 chipType - RaGene-1_0-st-v1

 cdf - AffymetrixCdfFile$byChipType(chipType, tags=r3)

 cs - AffymetrixCelSet$byName(tissues,cdf=cdf)


 print(cs)


 cs
 AffymetrixCelSet:
 Name: tissues
 Tags:
 Path: ../../arom-anal/rawData/tissues/RaGene-1_0-st-v1
 Platform: Affymetrix
 Chip type: RaGene-1_0-st-v1,r3
 Number of arrays: 8
 Names: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1), CS _
 7_(RaGene-1_0-st-v1), ..., NS _ 5_(RaGene-1_0-st-v1) [8]
 Time period: 2012-06-02 14:22:20 -- 2012-06-02 16:29:33
 Total file size: 84.50MB
 RAM: 0.01MB


 bc - RmaBackgroundCorrection(cs)

 csBC - process(bc,verbose=verbose)



 qn - QuantileNormalization(csBC, typesToUpdate = pm)

 print(qn)

 csN  - process(qn, verbose = verbose)

 plm - RmaPlm(csN)

 print(plm)



 Until here, looks fine, BUT, when i perform fit function as below and the
 errors come out related with directory,

 fit(plm, verbose = verbose)

 qam - QualityAssessmentModel(plm)

 #plotNuse(qam)

 plotRle(qam)



 current directory is /arom-anal, and setting up the data files (annotation,
 cel files, and raw data) look fine(see below hierarchical structure of
 directories),
 After you take a closer look at the following errors, could you please let
 me know what the problems are?



 Creating CEL file...done
 [2014-09-17 13:29:59] Exception: Pathname not found:
 arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/probeAffinities.CEL
 (none of the parent directories
 [arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/] exist; current
 directory is '/arom-anal')

   at #22. getReadablePathname.Arguments(static, ...)
   - getReadablePathname.Arguments() is in environment 'R.utils'

   at #21. getReadablePathname(static, ...)
   - getReadablePathname() is in environment 'R.utils'
   - originating from 'text'

   at #20. Arguments$getReadablePathname(filename, path = path, absolutePath
 = TRUE,
   mustExist = mustExist)
   - Arguments$getReadablePathname() is local of the calling function

   at #19. GenericDataFile(...)
   - GenericDataFile() is in environment 'R.filesets'

   at #18. extend(GenericDataFile(...), c(AromaMicroarrayDataFile,
 uses(FileCacheKeyInterface)))
   - extend() is in environment 'R.oo'

   at #17. AromaMicroarrayDataFile(...)
   - AromaMicroarrayDataFile() is in environment 'aroma.core'

   at #16. extend(AromaMicroarrayDataFile(...), c(AffymetrixFile,
 uses(AromaPlatformInterface)))
   - extend() is in environment 'R.oo'

   at #15. AffymetrixFile(...)
   - AffymetrixFile() is in environment 'aroma.affymetrix'

   at #14. extend(AffymetrixFile(...), AffymetrixCelFile, `cached:.header`
 = NULL,
   `cached:.lastPlotData` = NULL, .cdf = NULL)
   - extend() is in environment 'R.oo'

   at #13. AffymetrixCelFile(...)
   - AffymetrixCelFile() is in environment 'aroma.affymetrix'

   at #12. extend(AffymetrixCelFile(...), c(ParameterCelFile,
 uses(ParametersInterface)),
   `cached:.readUnitsCache` = NULL, encodeFunction =
 encodeFunction,
   decodeFunction = decodeFunction)
   - extend() is in environment 'R.oo'

   at #11. ParameterCelFile(...)
   - ParameterCelFile() is in environment 'aroma.affymetrix'

   at #10. extend(ParameterCelFile(...), ProbeAffinityFile,
 `cached:.firstCells` = NULL,
   probeModel = probeModel)
   - extend() is in environment 'R.oo'

   at #09. this(...)
   - this() is in environment 'aroma.affymetrix'

   at #08. newInstance.Class(.class, getPathname(paf), cdf = getCdf(ds),
   probeModel = this$probeModel)
   - newInstance.Class() is in environment 'R.oo'

   at #07. newInstance(.class, getPathname(paf), cdf = getCdf(ds), probeModel
 = this$probeModel)
   - newInstance() is in environment 'R.oo'

   at #06. getProbeAffinityFile.ProbeLevelModel(this, verbose =
 less(verbose))
   - getProbeAffinityFile.ProbeLevelModel() is in environment
 'aroma.affymetrix'

   at #05. NextMethod(getProbeAffinityFile)
   - NextMethod() is in environment 'base'

   at #04. getProbeAffinityFile.RmaPlm(this, verbose = less(verbose))
   - getProbeAffinityFile.RmaPlm() is in environment
 'aroma.affymetrix'

   at #03. getProbeAffinityFile(this, verbose = less(verbose))
   - getProbeAffinityFile() is in environment 'aroma.affymetrix'

   at #02. fit.ProbeLevelModel(plm, verbose = verbose)
   - fit.ProbeLevelModel() is in environment

Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)

2014-09-16 Thread Henrik Bengtsson

Ok, and then the output of:

path - getPath(plm)
print(path)
dir(plmData)
isDirectory(plmData)
Arguments$getReadablePath(plmData)

/H


On Tue, Sep 16, 2014 at 9:57 PM, jjspring OH sshshoh1...@gmail.com wrote:
 Hi Henrik,

 See below:


 print(plm)
 RmaPlm:
 Data set: tissues
 Chip type: RaGene-1_0-st-v1,r3
 Input tags: RBC,QN
 Output tags: RBC,QN,RMA
 Parameters: {probeModel: chr pm, shift: num 0, flavor: chr affyPLM,
 treatNAsAs: chr weights}
 Path: plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1
 RAM: 0.00MB
 print(getwd())
 [1] /arom-anal


 Thanks
 Sunghee


 2014년 9월 17일 수요일 오후 1시 45분 53초 UTC+9, Henrik Bengtsson 님의 말:

 That is really odd and I've never seen that error (8-9 years now).
 There must be a simple answer to this.  What does:

 print(plm)
 print(getwd())

 output when you get to that step.

 /Henrik


 On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH sshsh...@gmail.com wrote:
 
 
  Hi,
 
  After setting up the directory, performed background correction and rank
  based quantile normalization,
 
 
 
  library(aroma.affymetrix)
 
  verbose - Arguments$getVerbose(-8, timestamp=T)
 
  chipType - RaGene-1_0-st-v1
 
  cdf - AffymetrixCdfFile$byChipType(chipType, tags=r3)
 
  cs - AffymetrixCelSet$byName(tissues,cdf=cdf)
 
 
  print(cs)
 
 
  cs
  AffymetrixCelSet:
  Name: tissues
  Tags:
  Path: ../../arom-anal/rawData/tissues/RaGene-1_0-st-v1
  Platform: Affymetrix
  Chip type: RaGene-1_0-st-v1,r3
  Number of arrays: 8
  Names: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1), CS _
  7_(RaGene-1_0-st-v1), ..., NS _ 5_(RaGene-1_0-st-v1) [8]
  Time period: 2012-06-02 14:22:20 -- 2012-06-02 16:29:33
  Total file size: 84.50MB
  RAM: 0.01MB
 
 
  bc - RmaBackgroundCorrection(cs)
 
  csBC - process(bc,verbose=verbose)
 
 
 
  qn - QuantileNormalization(csBC, typesToUpdate = pm)
 
  print(qn)
 
  csN  - process(qn, verbose = verbose)
 
  plm - RmaPlm(csN)
 
  print(plm)
 
 
 
  Until here, looks fine, BUT, when i perform fit function as below and
  the
  errors come out related with directory,
 
  fit(plm, verbose = verbose)
 
  qam - QualityAssessmentModel(plm)
 
  #plotNuse(qam)
 
  plotRle(qam)
 
 
 
  current directory is /arom-anal, and setting up the data files
  (annotation,
  cel files, and raw data) look fine(see below hierarchical structure of
  directories),
  After you take a closer look at the following errors, could you please
  let
  me know what the problems are?
 
 
 
  Creating CEL file...done
  [2014-09-17 13:29:59] Exception: Pathname not found:
 
  arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/probeAffinities.CEL
  (none of the parent directories
  [arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/] exist; current
  directory is '/arom-anal')
 
at #22. getReadablePathname.Arguments(static, ...)
- getReadablePathname.Arguments() is in environment 'R.utils'
 
at #21. getReadablePathname(static, ...)
- getReadablePathname() is in environment 'R.utils'
- originating from 'text'
 
at #20. Arguments$getReadablePathname(filename, path = path,
  absolutePath
  = TRUE,
mustExist = mustExist)
- Arguments$getReadablePathname() is local of the calling
  function
 
at #19. GenericDataFile(...)
- GenericDataFile() is in environment 'R.filesets'
 
at #18. extend(GenericDataFile(...), c(AromaMicroarrayDataFile,
  uses(FileCacheKeyInterface)))
- extend() is in environment 'R.oo'
 
at #17. AromaMicroarrayDataFile(...)
- AromaMicroarrayDataFile() is in environment 'aroma.core'
 
at #16. extend(AromaMicroarrayDataFile(...), c(AffymetrixFile,
  uses(AromaPlatformInterface)))
- extend() is in environment 'R.oo'
 
at #15. AffymetrixFile(...)
- AffymetrixFile() is in environment 'aroma.affymetrix'
 
at #14. extend(AffymetrixFile(...), AffymetrixCelFile,
  `cached:.header`
  = NULL,
`cached:.lastPlotData` = NULL, .cdf = NULL)
- extend() is in environment 'R.oo'
 
at #13. AffymetrixCelFile(...)
- AffymetrixCelFile() is in environment 'aroma.affymetrix'
 
at #12. extend(AffymetrixCelFile(...), c(ParameterCelFile,
  uses(ParametersInterface)),
`cached:.readUnitsCache` = NULL, encodeFunction =
  encodeFunction,
decodeFunction = decodeFunction)
- extend() is in environment 'R.oo'
 
at #11. ParameterCelFile(...)
- ParameterCelFile() is in environment 'aroma.affymetrix'
 
at #10. extend(ParameterCelFile(...), ProbeAffinityFile,
  `cached:.firstCells` = NULL,
probeModel = probeModel)
- extend() is in environment 'R.oo'
 
at #09. this(...)
- this() is in environment 'aroma.affymetrix'
 
at #08. newInstance.Class(.class, getPathname(paf), cdf = getCdf(ds),
probeModel = this$probeModel)
- newInstance.Class() is in environment 'R.oo'
 
at #07.

Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)

2014-09-16 Thread jjspring OH




Hi Henrik,

See the outputs:

 path - getPath(plm) 
 print(path) 
[1] plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1
 dir(plmData) 
[1] tissues,RBC,QN,RMAtissues,RBC,QN,RMA,merged
 isDirectory(plmData) 
[1] TRUE
 Arguments$getReadablePath(plmData) 
[1] plmData












2014년 9월 17일 수요일 오후 2시 14분 45초 UTC+9, Henrik Bengtsson 님의 말:

 Ok, and then the output of: 

 path - getPath(plm) 
 print(path) 
 dir(plmData) 
 isDirectory(plmData) 
 Arguments$getReadablePath(plmData) 

 /H 


 On Tue, Sep 16, 2014 at 9:57 PM, jjspring OH sshsh...@gmail.com 
 javascript: wrote: 
  Hi Henrik, 
  
  See below: 
  
  
  print(plm) 
  RmaPlm: 
  Data set: tissues 
  Chip type: RaGene-1_0-st-v1,r3 
  Input tags: RBC,QN 
  Output tags: RBC,QN,RMA 
  Parameters: {probeModel: chr pm, shift: num 0, flavor: chr affyPLM, 
  treatNAsAs: chr weights} 
  Path: plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1 
  RAM: 0.00MB 
  print(getwd()) 
  [1] /arom-anal 
  
  
  Thanks 
  Sunghee 
  
  
  2014년 9월 17일 수요일 오후 1시 45분 53초 UTC+9, Henrik Bengtsson 님의 말: 
  
  That is really odd and I've never seen that error (8-9 years now). 
  There must be a simple answer to this.  What does: 
  
  print(plm) 
  print(getwd()) 
  
  output when you get to that step. 
  
  /Henrik 
  
  
  On Tue, Sep 16, 2014 at 9:38 PM, jjspring OH sshsh...@gmail.com 
 wrote: 
   
   
   Hi, 
   
   After setting up the directory, performed background correction and 
 rank 
   based quantile normalization, 
   
   
   
   library(aroma.affymetrix) 
   
   verbose - Arguments$getVerbose(-8, timestamp=T) 
   
   chipType - RaGene-1_0-st-v1 
   
   cdf - AffymetrixCdfFile$byChipType(chipType, tags=r3) 
   
   cs - AffymetrixCelSet$byName(tissues,cdf=cdf) 
   
   
   print(cs) 
   
   
   cs 
   AffymetrixCelSet: 
   Name: tissues 
   Tags: 
   Path: ../../arom-anal/rawData/tissues/RaGene-1_0-st-v1 
   Platform: Affymetrix 
   Chip type: RaGene-1_0-st-v1,r3 
   Number of arrays: 8 
   Names: CS _ 10_(RaGene-1_0-st-v1), CS _ 12_(RaGene-1_0-st-v1), CS _ 
   7_(RaGene-1_0-st-v1), ..., NS _ 5_(RaGene-1_0-st-v1) [8] 
   Time period: 2012-06-02 14:22:20 -- 2012-06-02 16:29:33 
   Total file size: 84.50MB 
   RAM: 0.01MB 
   
   
   bc - RmaBackgroundCorrection(cs) 
   
   csBC - process(bc,verbose=verbose) 
   
   
   
   qn - QuantileNormalization(csBC, typesToUpdate = pm) 
   
   print(qn) 
   
   csN  - process(qn, verbose = verbose) 
   
   plm - RmaPlm(csN) 
   
   print(plm) 
   
   
   
   Until here, looks fine, BUT, when i perform fit function as below and 
   the 
   errors come out related with directory, 
   
   fit(plm, verbose = verbose) 
   
   qam - QualityAssessmentModel(plm) 
   
   #plotNuse(qam) 
   
   plotRle(qam) 
   
   
   
   current directory is /arom-anal, and setting up the data files 
   (annotation, 
   cel files, and raw data) look fine(see below hierarchical structure 
 of 
   directories), 
   After you take a closer look at the following errors, could you 
 please 
   let 
   me know what the problems are? 
   
   
   
   Creating CEL file...done 
   [2014-09-17 13:29:59] Exception: Pathname not found: 
   
   
 arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/probeAffinities.CEL 
   (none of the parent directories 
   [arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/] exist; 
 current 
   directory is '/arom-anal') 
   
 at #22. getReadablePathname.Arguments(static, ...) 
 - getReadablePathname.Arguments() is in environment 
 'R.utils' 
   
 at #21. getReadablePathname(static, ...) 
 - getReadablePathname() is in environment 'R.utils' 
 - originating from 'text' 
   
 at #20. Arguments$getReadablePathname(filename, path = path, 
   absolutePath 
   = TRUE, 
 mustExist = mustExist) 
 - Arguments$getReadablePathname() is local of the calling 
   function 
   
 at #19. GenericDataFile(...) 
 - GenericDataFile() is in environment 'R.filesets' 
   
 at #18. extend(GenericDataFile(...), c(AromaMicroarrayDataFile, 
   uses(FileCacheKeyInterface))) 
 - extend() is in environment 'R.oo' 
   
 at #17. AromaMicroarrayDataFile(...) 
 - AromaMicroarrayDataFile() is in environment 'aroma.core' 
   
 at #16. extend(AromaMicroarrayDataFile(...), c(AffymetrixFile, 
   uses(AromaPlatformInterface))) 
 - extend() is in environment 'R.oo' 
   
 at #15. AffymetrixFile(...) 
 - AffymetrixFile() is in environment 'aroma.affymetrix' 
   
 at #14. extend(AffymetrixFile(...), AffymetrixCelFile, 
   `cached:.header` 
   = NULL, 
 `cached:.lastPlotData` = NULL, .cdf = NULL) 
 - extend() is in environment 'R.oo' 
   
 at #13. AffymetrixCelFile(...) 
 - AffymetrixCelFile() is in environment 'aroma.affymetrix' 
   
 at #12. extend(AffymetrixCelFile(...), c(ParameterCelFile, 
   uses(ParametersInterface)), 
 `cached:.readUnitsCache` =

Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)

Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)

Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)

Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)

Re: [aroma.affymetrix] [A problem on fitting a log additive probe level model (PLM)

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