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$probeModel)
>> > - newInstance.Class() is in environment 'R.oo'
>> >
>> > at #07. newInstance(.class, getPathname(paf), cdf = getCdf(ds),
>> > probeModel
>> > = this$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/.
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>> > To unsubscribe and other options, go to
>> > http://www.aroma-project.org/forum/
>> >
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>> > email to aroma-affymetr...@googlegroups.com.
>> > 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
> "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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--
--
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/.
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