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$probeModel)
> - newInstance() is in environment 'R.oo'
>
> at #06. getProbeAffinityFile.ProbeLevelModel(this, verbose =
> less(verbose))
> - getProbeAffinityFile.ProbeLevelModel() is in environment
> 'aroma.affymetrix'
>
> at #05. NextMethod("getProbeAffinityFile")
> - NextMethod() is in environment 'base'
>
> at #04. getProbeAffinityFile.RmaPlm(this, verbose = less(verbose))
> - getProbeAffinityFile.RmaPlm() is in environment
> 'aroma.affymetrix'
>
> at #03. getProbeAffinityFile(this, verbose = less(verbose))
> - getProbeAffinityFile() is in environment 'aroma.affymetrix'
>
> at #02. fit.ProbeLevelModel(plm, verbose = verbose)
> - fit.ProbeLevelModel() is in environment 'aroma.affymetrix'
>
> at #01. fit(plm, verbose = verbose)
> - fit() is in environment 'aroma.core'
>
> Error: Pathname not found:
> arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/probeAffinities.CEL
> (none of the parent directories
> [arom-anal/plmData/tissues,RBC,QN,RMA/RaGene-1_0-st-v1/] exist; current
> directory is '/arom-anal')
> In addition: Warning messages:
> 1: In is.na(parent) :
> is.na() applied to non-(list or vector) of type 'NULL'
> 2: In is.na(parent) :
> is.na() applied to non-(list or vector) of type 'NULL'
> 20140917 13:29:59| Setting up parameter sets...done
> 20140917 13:29:59|Fitting model of class RmaPlm...done
>
> verdas-MacBook-Pro:arom-anal sungheeoh$ ls -R | grep ":$" | sed -e 's/:$//'
> -e 's/[^-][^\/]*\//--/g' -e 's/^/ /' -e 's/-/|/'
> |-annotationData
> |---chipTypes
> |-----RaGene-1_0-st-v1
> |-plmData
> |---tissues,RBC,QN,RMA
> |-----RaGene-1_0-st-v1
> |-probeData
> |---tissues,QN
> |-----RaGene-1_0-st-v1
> |---tissues,RBC
> |-----RaGene-1_0-st-v1
> |---tissues,RBC,QN
> |-----RaGene-1_0-st-v1
> |-rawData
> |---tissues
> |-----RaGene-1_0-st-v1
>
>
>
>
>
>> sessionInfo()
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [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!
>
> Sunghee
>
>
> --
> --
> 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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>
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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/
---
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