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

[Valerie Obenchain]

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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