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,RMA" "tissues,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$getReadablePathname() is local of the calling
> >> > function
> >> >
> >> > at #19. GenericDataFile(...)
> >> > - GenericDataFile() is in environment 'R.filesets'
> >> >
> >> > at #18. extend(GenericDataFile(...), c("AromaMicroarrayDataFile",
> >> > uses("FileCacheKeyInterface")))
> >> > - extend() is in environment 'R.oo'
> >> >
> >> > at #17. AromaMicroarrayDataFile(...)
> >> > - AromaMicroarrayDataFile() is in environment 'aroma.core'
> >> >
> >> > at #16. extend(AromaMicroarrayDataFile(...), c("AffymetrixFile",
> >> > uses("AromaPlatformInterface")))
> >> > - extend() is in environment 'R.oo'
> >> >
> >> > at #15. AffymetrixFile(...)
> >> > - AffymetrixFile() is in environment 'aroma.affymetrix'
> >> >
> >> > at #14. extend(AffymetrixFile(...), "AffymetrixCelFile",
> >> > `cached:.header`
> >> > = NULL,
> >> > `cached:.lastPlotData` = NULL, .cdf = NULL)
> >> > - extend() is in environment 'R.oo'
> >> >
> >> > at #13. AffymetrixCelFile(...)
> >> > - AffymetrixCelFile() is in environment 'aroma.affymetrix'
> >> >
> >> > at #12. extend(AffymetrixCelFile(...), c("ParameterCelFile",
> >> > uses("ParametersInterface")),
> >> > `cached:.readUnitsCache` = NULL, encodeFunction =
> >> > encodeFunction,
> >> > decodeFunction = decodeFunction)
> >> > - extend() is in environment 'R.oo'
> >> >
> >> > at #11. ParameterCelFile(...)
> >> > - ParameterCelFile() is in environment 'aroma.affymetrix'
> >> >
> >> > at #10. extend(ParameterCelFile(...), "ProbeAffinityFile",
> >> > `cached:.firstCells` = NULL,
> >> > probeModel = probeModel)
> >> > - extend() is in environment 'R.oo'
> >> >
> >> > at #09. this(...)
> >> > - this() is in environment 'aroma.affymetrix'
> >> >
> >> > at #08. newInstance.Class(.class, getPathname(paf), cdf =
> getCdf(ds),
> >> > probeModel = this$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.
> >> >
> >> >
> >> > 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-af...@googlegroups.com
> >> > To unsubscribe and other options, go to
> >> > http://www.aroma-project.org/forum/
> >> >
> >> > ---
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> send
> >> > an
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> >> > For more options, visit https://groups.google.com/d/optout.
> >
> > --
> > --
> > 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
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> > To post to this group, send email to aroma-af...@googlegroups.com
> <javascript:>
> > To unsubscribe and other options, go to
> http://www.aroma-project.org/forum/
> >
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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.
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