Hi Henrik,
Thanks for you email. Here is the problem I encountered.
I installed the package using, it is the latest version 3.0.0
source('http://callr.org/install#aroma.affymetrix')
and I was trying to run doCRMAv2
dsList <- doCRMAv2(cel.subset, cdf=cdf,
verbose=Arguments$getVerbose(-10, timestamp=TRUE))
and then got error information
> <simpleError: Argument 'centers' for matrixStats::rowMads() has been
renamed
> to 'center'. Please update code accordingly.>
>
> [2016-03-24 13:12:44] Exception: The fit function for requested AvgPlm
> flavor failed: median
>
>
>
>
> at #08. getFitUnitGroupFunction.AvgPlm(this, ...)
>
> - getFitUnitGroupFunction.AvgPlm() is in environment
> 'aroma.affymetrix'
>
>
>
>
> at #07. getFitUnitGroupFunction(this, ...)
>
> - getFitUnitGroupFunction() is in environment 'aroma.affymetrix'
>
>
>
>
> at #06. getFitUnitFunction.CnPlm(this)
>
> - getFitUnitFunction.CnPlm() is in environment
'aroma.affymetrix'
>
>
>
>
> at #05. getFitUnitFunction(this)
>
> - getFitUnitFunction() is in environment 'aroma.affymetrix'
>
>
>
>
> at #04. fit.ProbeLevelModel(plm, verbose = verbose)
>
> - fit.ProbeLevelModel() is in environment 'aroma.affymetrix'
>
>
>
>
> at #03. fit(plm, verbose = verbose)
>
> - fit() is in environment 'aroma.core'
>
>
>
>
> at #02. doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose =
> Arguments$getVerbose(-10,
>
> timestamp = TRUE))
>
> - doCRMAv2.AffymetrixCelSet() is in environment
'aroma.affymetrix'
>
>
>
>
> at #01. doCRMAv2(cel.subset, cdf = cdf, verbose =
> Arguments$getVerbose(-10,
>
> timestamp = TRUE))
>
> - doCRMAv2() is in environment 'aroma.affymetrix'
>
>
>
>
> Error: The fit function for requested AvgPlm flavor failed: median
>
> 20160324 13:12:44| Setting up parameter sets...done
>
> 20160324 13:12:44| Fitting model of class AvgCnPlm...done
>
>>
>
traceback()
>
> 13: stop(cond)
>
> 12: throw.Exception(Exception(...))
>
> 11: throw(Exception(...))
>
> 10: throw.default("The fit function for requested AvgPlm flavor failed: ",
>
> flavor)
>
> 9: throw("The fit function for requested AvgPlm flavor failed: ",
>
> flavor)
>
> 8: getFitUnitGroupFunction.AvgPlm(this, ...)
>
> 7: getFitUnitGroupFunction(this, ...)
>
> 6: getFitUnitFunction.CnPlm(this)
>
> 5: getFitUnitFunction(this)
>
> 4: fit.ProbeLevelModel(plm, verbose = verbose)
>
> 3: fit(plm, verbose = verbose)
>
> 2: doCRMAv2.AffymetrixCelSet(cel.subset, cdf = cdf, verbose = v)
>
> 1: doCRMAv2(cel.subset, cdf = cdf, verbose = v)
>
>
sessionInfo()
>
> R version 3.1.0 (2014-04-10)
>
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
>
> locale:
>
> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
> LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915
> LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915
> LC_PAPER=en_US.iso885915
>
> [8] LC_NAME=C LC_ADDRESS=C
> LC_TELEPHONE=C LC_MEASUREMENT=en_US.iso885915
> LC_IDENTIFICATION=C
>
>
> attached base packages:
>
> [1] stats graphics grDevices utils datasets methods base
>
>
> other attached packages:
>
> [1] sfit_0.3.0 aroma.light_2.0.0 matrixStats_0.50.1
> aroma.affymetrix_2.13.1 aroma.core_2.13.0 R.devices_2.14.0
> R.filesets_2.6.0 R.utils_2.2.0 R.oo_1.20.0
> affxparser_1.36.0
>
> [11] R.methodsS3_1.7.1
>
>
> loaded via a namespace (and not attached):
>
> [1] aroma.apd_0.6.0 base64enc_0.1-4 digest_0.6.9 DNAcopy_1.38.1
> PSCBS_0.43.0 R.cache_0.12.0 R.huge_0.9.0 R.rsp_0.21.0
tools_3.1.0
>
>
On Thursday, March 24, 2016 at 12:22:36 PM UTC-7, Henrik Bengtsson wrote:
>
> Hi, in order for us to help you, could you please:
>
> "[...] 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."
>
> Thanks,
>
> Henrik
>
> On Thu, Mar 24, 2016 at 9:59 AM, C.C. <chenc...@gmail.com <javascript:>>
> wrote:
> > Hello,
> >
> > I was trying to run doCRMAv2.R in aroma.affymetrix 3.0 and get the
> error.
> > Dose anyone know what is the problem? Thanks.
> >
> >
> >
> > Error: The fit function for requested AvgPlm flavor failed: median
> >
> > --
> > --
> > 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/
> >
> > ---
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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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