doCRMAv2, Error: The fit function for requested AvgPlm flavor failed: median

[C.C.]

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

[Henrik Bengtsson]

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

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> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
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[C.C.]

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

[Henrik Bengtsson]

On Thu, Mar 24, 2016 at 1:54 PM, C.C. <chenc...@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

[Henrik Bengtsson]

You most likely got an error during installation, because
aroma.affymetrix now requires R (≥ 3.1.2) -
https://cran.r-project.org/web/packages/aroma.affymetrix/ - and you're
on R 3.1.0, which is nearly two years old.

The solution is to update to a recent version of R, i.e. R 3.2.4.
FYI, R 3.3.0 is coming in a few weeks.

/Henrik

[C.C.]

I installed R 3.2.3 (don't know why unable to install R 3.2.4) and then reinstalled aroma.affymetrix 3.0. It worked!

Thanks Henrik!

[Henrik Bengtsson]

Good to hear. /Henrik