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]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >