On Thu, Mar 24, 2016 at 1:54 PM, C.C. <chenchen...@gmail.com> wrote:
> 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')
Did you get errors and did you make sure you restarted R, because your
session information below says you're still running lots of outdated
versions, e.g. aroma.affymetrix_2.13.1.
/Henrik
>
>
>
> 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> 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
>> > 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/.
> 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/.
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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