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
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