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


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

chipType <- "RaGene-1_0-st-v1"

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

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


> cs
Name: tissues
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")


csN  <- process(qn, verbose = verbose)

plm <- RmaPlm(csN)


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)



current directory is /arom-anal, and setting up the data files (annotation, 
cel files, and raw data) look fine(see below hierarchical structure of 
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: 
(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", 
          - extend() is in environment 'R.oo'

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

  at #16. extend(AromaMicroarrayDataFile(...), c("AffymetrixFile", 
          - 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", 
              `cached:.readUnitsCache` = NULL, 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 = 
          - getProbeAffinityFile.ProbeLevelModel() is in environment 

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

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

  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 'aroma.affymetrix'

  at #01. fit(plm, verbose = verbose)
          - fit() is in environment 'aroma.core'

Error: Pathname not found: 
(none of the parent directories 
[arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/] exist; current 
directory is '/arom-anal')
In addition: Warning messages:
1: In is.na(parent) :
  is.na() applied to non-(list or vector) of type 'NULL'
2: In is.na(parent) :
  is.na() applied to non-(list or vector) of type 'NULL'
20140917 13:29:59| Setting up parameter sets...done
20140917 13:29:59|Fitting model of class RmaPlm...done

verdas-MacBook-Pro:arom-anal sungheeoh$ ls -R | grep ":$" | sed -e 's/:$//' 
-e 's/[^-][^\/]*\//--/g' -e 's/^/   /' -e 's/-/|/'

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] preprocessCore_1.26.1   Biostrings_2.32.1       XVector_0.4.0          
 [4] Biobase_2.24.0          oligoClasses_1.26.0     BiocGenerics_0.10.0    
 [7] BiocInstaller_1.14.2    aroma.light_2.0.0       matrixStats_0.10.0     
[10] aroma.affymetrix_2.12.0 aroma.core_2.12.1       R.devices_2.11.0       
[13] R.filesets_2.6.0        R.utils_1.33.0          R.oo_1.18.0            
[16] oligo_1.28.2            IRanges_1.22.10         affxparser_1.36.0      
[19] R.methodsS3_1.6.1      

loaded via a namespace (and not attached):
 [1] affyio_1.32.0        aroma.apd_0.5.0      base64enc_0.1-2     
 [4] bit_1.1-12           codetools_0.2-9      DBI_0.3.0           
 [7] digest_0.6.4         DNAcopy_1.38.1       ff_2.2-13           
[10] foreach_1.4.2        GenomeInfoDb_1.0.2   GenomicRanges_1.16.4
[13] iterators_1.0.7      PSCBS_0.43.0         R.cache_0.10.0      
[16] R.huge_0.8.0         R.rsp_0.19.0         splines_3.1.1       
[19] stats4_3.1.1         tools_3.1.1          zlibbioc_1.10.0   

Thanks in advance!


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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