Hello List I have a set of Rat Gene ST CEL files to analyse and have started looking into using xps for this. I have begun by building the required scheme file for the arrays. I have downloaded the relevant files from affymetrix (RaGene-1_0-st-v1.r4.clf, RaGene-1_0-st-v1.r4.pgf, RaGene- 1_0-st-v1.na32.rn4.probeset.csv & RaGene- 1_0-st-v1.na32.rn4.transcript.csv) and built the scheme file as follows: libdir <- paste(getwd(), 'xpsAnalysis/annotationFiles', sep='/') # the annotation files are here xps.scheme <- import.exon.scheme('Scheme_RaGene10stv1r4', filedir=paste(getwd(), 'xpsAnalysis/rootScheme', sep='/'), layoutfile = paste(libdir,'RaGene-1_0-st-v1.r4.clf', sep='/'), schemefile = paste(libdir,'RaGene-1_0-st-v1.r4.pgf',sep='/'), probeset = paste(libdir,'RaGene-1_0-st-v1.na32.rn4.probeset.csv', sep='/'), transcript = paste(libdir, 'RaGene-1_0-st-v1.na32.rn4.transcript.csv', sep='/')) # create the scheme Note that I use the import.exon.scheme command as per advice from cstrato for the r4 annotation files (some weblink I can't find just now). This goes well and I get a .root file in the right directory. However I noticed that during the process the following warning is issued: Importing as <ragene-1_0-st-v1.anp>... Note: The following header columns are missing or in wrong order:    <mouse_fl>    <mouse_mrna>    <rat_fl>    <rat_mrna> Something to be concerned about? I'm not sure what the mouse data would be doing in the annotations for the rat chips but I'm not yet familiar with the platform. Advice appreciated. Thanks iain > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-pc-linux-gnu (64-bit) locale:  [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C  [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8  [5] LC_MONETARY=en_GB.utf8    LC_MESSAGES=en_GB.utf8  [7] LC_PAPER=C                LC_NAME=C  [9] LC_ADDRESS=C              LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats     graphics  grDevices utils     datasets  methods   base other attached packages: [1] xps_1.16.0 loaded via a namespace (and not attached): [1] tools_2.15.0 [[alternative HTML version deleted]]

Dear Iain, Everything is ok, this is just a note (and not a warning message) where I list the columns from the Affymetrix annotation file(s) which have somehow changed or were deleted by Affymetrix. The reason is that during the years Affymetrix has changed/added/deleted columns from their annotation files, so this is mainly an information for me. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._ On 6/20/12 5:42 PM, Iain Gallagher wrote: > Hello List > > I have a set of Rat Gene ST CEL files to analyse and have started looking into using xps for this. I have begun by building the required scheme file for the arrays. I have downloaded the relevant files from affymetrix (RaGene-1_0-st-v1.r4.clf, RaGene-1_0-st-v1.r4.pgf, RaGene- 1_0-st-v1.na32.rn4.probeset.csv& RaGene- 1_0-st-v1.na32.rn4.transcript.csv) and built the scheme file as follows: > > libdir<- paste(getwd(), 'xpsAnalysis/annotationFiles', sep='/') # the annotation files are here > > xps.scheme<- import.exon.scheme('Scheme_RaGene10stv1r4', filedir=paste(getwd(), 'xpsAnalysis/rootScheme', sep='/'), layoutfile = paste(libdir,'RaGene-1_0-st-v1.r4.clf', sep='/'), schemefile = paste(libdir,'RaGene-1_0-st-v1.r4.pgf',sep='/'), probeset = paste(libdir,'RaGene-1_0-st-v1.na32.rn4.probeset.csv', sep='/'), transcript = paste(libdir, 'RaGene-1_0-st-v1.na32.rn4.transcript.csv', sep='/')) # create the scheme > > > Note that I use the import.exon.scheme command as per advice from cstrato for the r4 annotation files (some weblink I can't find just now). > > > This goes well and I get a .root file in the right directory. However I noticed that during the process the following warning is issued: > > Importing as<ragene-1_0-st-v1.anp>... > Note: The following header columns are missing or in wrong order: > <mouse_fl> > <mouse_mrna> > <rat_fl> > <rat_mrna> > > > Something to be concerned about? > > I'm not sure what the mouse data would be doing in the annotations for the rat chips but I'm not yet familiar with the platform. > > Advice appreciated. > > Thanks > > iain > >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C > [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8 > [5] LC_MONETARY=en_GB.utf8 LC_MESSAGES=en_GB.utf8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] xps_1.16.0 > > loaded via a namespace (and not attached): > [1] tools_2.15.0 > [[alternative HTML version deleted]] > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor