[BioC] Results of QC of Demodata included in the package HumMeth27QCReport

[Valerie Obenchain]

Hi Francesco,

Thanks for fixing the DemoData. When answering a question on the mailing 
list, please respond to the original email (ie, either Greg's message or 
my mine). That way all messages of the same topic are kept together in 
thread form or by subject. This will make it easier for people searching 
the list in the future to find all related information.

Thanks,
Valerie


On 11/24/10 04:23, Francesco Mancuso wrote:
>
> 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. 









On 11/23/10 09:34, Valerie Obenchain wrote:
> 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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>
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