LumiBatch objects contain two slots (controlData and QC) which are not mentioned on the documentation page help("LumiBatch-class"). Yet they don't contain the slot "summary" which is described on the help page. What are controlData and QC and how are they used? Is summary defunct? Gordon > library(lumi) > a <- new("LumiBatch") > slotNames(a) [1] "history" "controlData" "QC" "assayData" [5] "phenoData" "featureData" "experimentData" "annotation" [9] ".__classVersion__" > sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_M ONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia. 1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] lumi_1.4.0 annotate_1.16.0 xtable_1.5-1 AnnotationDbi_1.0.0 [5] RSQLite_0.6-3 DBI_0.2-3 mgcv_1.3-27 affy_1.16.0 [9] preprocessCore_1.0.0 affyio_1.6.0 Biobase_1.16.0

Thanks for pointing out this! Gordon I will add the description of these two slots in the LumiBatch documentation. Also I will add them in the summary returns. Pan On 10/26/07 5:00 AM, "bioconductor-request at stat.math.ethz.ch" <bioconductor-request at="" stat.math.ethz.ch=""> wrote: > Message: 19 > Date: Fri, 26 Oct 2007 18:25:21 +1000 > From: Gordon Smyth <smyth at="" wehi.edu.au=""> > Subject: [BioC] lumi: LumiBatch slots don't match documentation > To: "BioC Mailing List" <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <6.2.5.6.1.20071026182011.01f2b8e0 at wehi.edu.au> > Content-Type: text/plain; charset="us-ascii"; format=flowed > > LumiBatch objects contain two slots (controlData and QC) which are > not mentioned on the documentation page help("LumiBatch-class"). Yet > they don't contain the slot "summary" which is described on the help page. > > What are controlData and QC and how are they used? > > Is summary defunct? > > Gordon > >> library(lumi) >> a <- new("LumiBatch") >> slotNames(a) > [1] > "history" "controlData" "QC" "assayData" > [5] > "phenoData" "featureData" "experimentData" "annotation" > [9] ".__classVersion__" > >> sessionInfo() > R version 2.6.0 (2007-10-03) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC _MONETARY= > English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252 > > attached base packages: > [1] tools stats graphics grDevices > utils datasets methods base > > other attached packages: > [1] > lumi_1.4.0 annotate_1.16.0 xtable_1.5-1 > AnnotationDbi_1.0.0 > [5] > RSQLite_0.6-3 DBI_0.2-3 mgcv_1.3-27 > affy_1.16.0 > [9] preprocessCore_1.0.0 affyio_1.6.0 Biobase_1.16.0 > > >