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
> <javascript:>> 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
> <javascript:>
> > To unsubscribe and other options, go to
> http://www.aroma-project.org/forum/
> >
> > ---
> > You received this message because you are subscribed to the Google
> Groups
> > "aroma.affymetrix" group.
> > To unsubscribe from this group and stop receiving emails from it, send
> an
> > email to aroma-affymetr...@googlegroups.com <javascript:>.
> > 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/
---
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to aroma-affymetrix+unsubscr...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
