Dear Bioconductors, I am just looking through one of the vignettes with the /oligo/ package (V1Overview.pdf). I have downloaded the test data from the Affymetrix link and am following the commands in the pdf: library(pd.hg.u95a) library(oligo) celfiles <- list.celfiles(getwd()) affyExpressionFS <- read.celfiles(celfiles) > class(affyExpressionFS) [1] "ExpressionFeatureSet" attr(,"package") [1] "oligoClasses" but then I get to: > pmSeq <- pmSequence(affyExpressionFS) Warning message: In .local(object, ...) : pmSequence.rda file is not available for this pdInfo pkg. > pmSeq NULL pmSequence.rda is available, in Rdata.zip in R\R-2.11.0\library\pd.hg.u95a\data. Any ideas how I can get R to realise that it is available? With thanks for your time, Lavinia Gordon. > sessionInfo() R version 2.11.0 (2010-04-22) i386-pc-mingw32 locale: [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 LC_MONETARY=English_Australia.1252 [4] LC_NUMERIC=C LC_TIME=English_Australia.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.hg.u95a_0.99.0 oligo_1.12.2 oligoClasses_1.10.0 Biobase_2.8.0 RSQLite_0.9-2 DBI_0.2-5 loaded via a namespace (and not attached): [1] affxparser_1.20.0 affyio_1.16.0 Biostrings_2.16.4 IRanges_1.6.6 preprocessCore_1.10.0 [6] splines_2.11.0 tools_2.11.0 -- Senior Bioinformatics Officer Murdoch Childrens Research Institute Royal Children's Hospital Flemington Road Parkville Victoria 3052 Australia www.mcri.edu.au [[alternative HTML version deleted]]

Hi Lavinia, thanks for the report, I'll have this fixed ASAP. benilton On 10 August 2010 03:32, Lavinia Gordon <lavinia.gordon at="" mcri.edu.au=""> wrote: > Dear Bioconductors, > > I am just looking through one of the vignettes with the /oligo/ package > (V1Overview.pdf). > I have downloaded the test data from the Affymetrix link and am > following the commands in the pdf: > > library(pd.hg.u95a) > library(oligo) > celfiles <- list.celfiles(getwd()) > affyExpressionFS <- read.celfiles(celfiles) > ?> class(affyExpressionFS) > [1] "ExpressionFeatureSet" > attr(,"package") > [1] "oligoClasses" > > but then I get to: > ?> pmSeq <- pmSequence(affyExpressionFS) > Warning message: > In .local(object, ...) : > ? pmSequence.rda file is not available for this pdInfo pkg. > > ?> pmSeq > NULL > > pmSequence.rda is available, in Rdata.zip in > R\R-2.11.0\library\pd.hg.u95a\data. ?Any ideas how I can get R to > realise that it is available? > > With thanks for your time, > > Lavinia Gordon. > > ?> sessionInfo() > R version 2.11.0 (2010-04-22) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_Australia.1252 > LC_CTYPE=English_Australia.1252 ? ?LC_MONETARY=English_Australia.1252 > [4] LC_NUMERIC=C ? ? ? ? ? ? ? ? ? ? ? LC_TIME=English_Australia.1252 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] pd.hg.u95a_0.99.0 ? oligo_1.12.2 ? ? ? ?oligoClasses_1.10.0 > Biobase_2.8.0 ? ? ? RSQLite_0.9-2 ? ? ? DBI_0.2-5 > > loaded via a namespace (and not attached): > [1] affxparser_1.20.0 ? ? affyio_1.16.0 ? ? ? ? Biostrings_2.16.4 > IRanges_1.6.6 ? ? ? ? preprocessCore_1.10.0 > [6] splines_2.11.0 ? ? ? ?tools_2.11.0 > > -- > Senior Bioinformatics Officer > Murdoch Childrens Research Institute > Royal Children's Hospital > Flemington Road > Parkville > Victoria 3052 > Australia > www.mcri.edu.au > > > ? ? ? ?[[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 >