[BioC] Results of QC of Demodata included in the package, HumMeth27QCReport
Francesco Mancuso
francesco.mancuso at crg.es
Wed Nov 24 13:23:25 CET 2010
Hi!
There was a problem in the DemoData.
The only thing that was affected was the excel file with the summary of
the QC, not the plots.
I have just uploaded in CRAN a new version of the package in which this
problem is solved. I think that tomorrow it will be available.
Regarding the normalization, as Sean Davis suggested me, in version 1.1
I substituted the methylumi normalization (meant for GoldenGate
platform) with the normalization from lumi.
Now what you export are the normalized log2 ratios.
Best,
Francesco
PS I don't know if this mailing list is the correct place to discuss
about packages from another repository. If you think not, please contact
me directly.
> ------------------------------
>
> Message: 7
> Date: Mon, 22 Nov 2010 21:54:33 +0000 (GMT)
> From: gregory voisin<voisingreg at yahoo.fr>
> To: bioconductor<bioconductor at stat.math.ethz.ch>
> Subject: [BioC] Results of QC of Demodata included in the package
> HumMeth27QCReport
> Message-ID:<448764.65103.qm at web29520.mail.ird.yahoo.com>
> Content-Type: text/plain
>
> hi,
> when I use the function "HumMeth27QCReport" on the demodata included in the
> package HumMeth27QCReport, I get the message.
>
>
> Erreur dans data.frame(Index = samps2$Index, `Sample ID` = samps2$SampleID, :
> arguments imply differing number of rows: 12, 0
> De plus : Message d'avis :
> In normalizeMethyLumiSet(mldat[, toKeep]) :
> This function is probably not optimal for Infinium data and is meant
> for GoldenGate methylation data only.
>
> But in my folder , this function generate the interest graphs for QC.
> Have this message some consequencies on the interpretation or the result of QC ?
>
> Greg
> Montreal
>
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=French_Canada.1252 LC_CTYPE=French_Canada.1252
> [3] LC_MONETARY=French_Canada.1252 LC_NUMERIC=C
> [5] LC_TIME=French_Canada.1252
>
> attached base packages:
> [1] tcltk grid splines stats graphics grDevices utils
> [8] datasets methods base
>
> other attached packages:
> [1] HumMeth27QCReport_1.0 WriteXLS_2.1.0 plotrix_3.0-2
> [4] gplots_2.8.0 caTools_1.10 bitops_1.0-4.1
> [7] gdata_2.8.0 gtools_2.6.2 Hmisc_3.8-3
> [10] survival_2.35-8 methylumi_1.6.1 amap_0.8-5
> [13] Biobase_2.10.0
>
> loaded via a namespace (and not attached):
> [1] cluster_1.13.1 lattice_0.19-13 tools_2.12.0
>
>
>
>
> [[alternative HTML version deleted]]
>
>
>
> ------------------------------
>
> Message: 8
> Date: Tue, 23 Nov 2010 09:34:52 -0800
> From: Valerie Obenchain<vobencha at fhcrc.org>
> To: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Results of QC of Demodata included in the package
> HumMeth27QCReport
> Message-ID:<4CEBFB3C.8080300 at fhcrc.org>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Greg,
>
> I get the same error,
>
> > dir<- system.file("DemoData", package="HumMeth27QCReport")
> > HumMeth27QCReport(dir)
> Perform quantile color balance adjustment ...
> Perform quantile normalization ...
> Error in data.frame(Index = samps2$Index, `Sample ID` = samps2$SampleID, :
> arguments imply differing number of rows: 12, 0
>
>
> It looks like there is a problem with the sample data or the package
> code. This is a CRAN package, not BioC. I would contact the maintainer
> directly since they may not be reading this mailing list,
> francesco.mancuso at crg.es
>
>
> Valerie
>
> > sessionInfo()
> R version 2.13.0 Under development (unstable) (2010-10-23 r53398)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] tcltk grid splines stats graphics grDevices utils
> [8] datasets methods base
>
> other attached packages:
> [1] IlluminaHumanMethylation27k.db_1.4.0 org.Hs.eg.db_2.4.6
> [3] RSQLite_0.9-3 DBI_0.2-5
> [5] AnnotationDbi_1.13.7 HumMeth27QCReport_1.1
> [7] WriteXLS_2.1.0 plotrix_3.0-3
> [9] gplots_2.8.0 caTools_1.10
> [11] bitops_1.0-4.1 gdata_2.8.1
> [13] gtools_2.6.2 Hmisc_3.8-3
> [15] survival_2.36-2 amap_0.8-5
> [17] lumi_2.3.0 methylumi_1.7.1
> [19] Biobase_2.11.6
>
> loaded via a namespace (and not attached):
> [1] KernSmooth_2.23-4 MASS_7.3-8 Matrix_0.999375-45
> [4] affy_1.29.1 affyio_1.19.2 annotate_1.29.2
> [7] cluster_1.13.2 hdrcde_2.15 lattice_0.19-13
> [10] mgcv_1.7-2 nlme_3.1-97 preprocessCore_1.13.1
> [13] xtable_1.5-6
>
>
>
> On 11/22/10 13:54, gregory voisin wrote:
>> hi,
>> when I use the function "HumMeth27QCReport" on the demodata included in the
>> package HumMeth27QCReport, I get the message.
>>
>>
>> Erreur dans data.frame(Index = samps2$Index, `Sample ID` = samps2$SampleID, :
>> arguments imply differing number of rows: 12, 0
>> De plus : Message d'avis :
>> In normalizeMethyLumiSet(mldat[, toKeep]) :
>> This function is probably not optimal for Infinium data and is meant
>> for GoldenGate methylation data only.
>>
>> But in my folder , this function generate the interest graphs for QC.
>> Have this message some consequencies on the interpretation or the result of QC ?
>>
>> Greg
>> Montreal
>>
>>
>>> sessionInfo()
>>>
>> R version 2.12.0 (2010-10-15)
>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>>
>> locale:
>> [1] LC_COLLATE=French_Canada.1252 LC_CTYPE=French_Canada.1252
>> [3] LC_MONETARY=French_Canada.1252 LC_NUMERIC=C
>> [5] LC_TIME=French_Canada.1252
>>
>> attached base packages:
>> [1] tcltk grid splines stats graphics grDevices utils
>> [8] datasets methods base
>>
>> other attached packages:
>> [1] HumMeth27QCReport_1.0 WriteXLS_2.1.0 plotrix_3.0-2
>> [4] gplots_2.8.0 caTools_1.10 bitops_1.0-4.1
>> [7] gdata_2.8.0 gtools_2.6.2 Hmisc_3.8-3
>> [10] survival_2.35-8 methylumi_1.6.1 amap_0.8-5
>> [13] Biobase_2.10.0
>>
>> loaded via a namespace (and not attached):
>> [1] cluster_1.13.1 lattice_0.19-13 tools_2.12.0
>>
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>
>
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