On Jul 4, 2008, at 1:36 AM, DAVID ARTETA GARCIA wrote: > Dear list, please apologise for not providing enough information. > >> sessionInfo() > R version 2.7.0 (2008-04-22) > i386-pc-mingw32 > > attached base packages: > [1] grid tools stats graphics grDevices utils > datasets methods base > > other attached packages: > [1] arrayQuality_1.18.0 RColorBrewer_1.0-2 gridBase_0.4-3 > hexbin_1.14.0 convert_1.16.0 marray_1.18.0 > vsn_3.6.0 > [8] limma_2.14.0 lattice_0.17-6 affy_1.18.0 > preprocessCore_1.2.0 affyio_1.8.0 Biobase_2.0.0 > > > I have 12 one-color gpr files. These were loaded using limma?s > read.maimages() > >> data = read.maimages(filenames,source="genepix") > Read 0023.gpr > Read 0024.gpr > Read 0025.gpr > . > . > > data > An object of class "RGList" > > I then transformed R and Rg to NULL as suggested on this list (after > searching in the archives). > > I actually tried vsn normalisation of G values using the most recent > vsn2() function ( I guess I could have also used justvsn()). If I am > not wrong, vsn2 can take a matrix as argument: > > data.norm = vsn2(data2$G) > vsn: 2352 x 12 matrix (1 stratum). 0% done. > 14% done. > 28% done. > 42% done. > 57% done. > 71% done. > 85% done. > 100% done. > Please use 'meanSdPlot' to verify the fit. > > but I also wanted to check wether there was an improvement > correcting for backgroung effects since I can see a spatial trend on > some of the chips. I read on the vsn vignette that the argument > "backgroundsubtract" to justvsn might take care of this trend, but > of course, the function could not find "R": > > data.vsn_b<-justvsn(data2,backgroundsubtract=TRUE) > Error in eval(expr, envir, enclos) : object "R" not found > Error in is(object, Cl) : > error in evaluating the argument 'x' in selecting a method for > function 'vsn2' > > Maybe I should leave R and Rg as they are (all 0?s) instead of NULL- > ing them? The background subtraction vsn does is really just (in your case) vsn2(data$G - data$Gb) provided that the Gb slot holds the estimated local background (whether that is true depends on how you have read the files, I am not too familiar with GenePix). Kasper > I haven?t tried converting to an ExpressionSet which I thought was > mainly for affy data, but how can I handle both the foreground G and > background Gb data in the ExpressionSet? I haven?t confronted this > matter before. > > Thanks, > > D. > > Quoting Wolfgang Huber <huber at="" ebi.ac.uk="">: >> >> >> Dear David, >> >> please provide the output of sessionInfo() and a reproducible >> example, >> otherwise it is difficult to give a concrete reply. >> >> Also, please use the function "vsn2" instead of "vsn" (both in the >> package vsn). >> >> From your message it appears (sorry if my guess is wrong - see above) >> as if you use an RGList for one color data - which, if true, would be >> weird. Have you tried putting the data into an ExpressionSet and then >> calling vsn2/justvsn on that? >> >> Best wishes >> Wolfgang >> >> >> -- >> ---------------------------------------------------- >> Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber >> >> >> DAVID ARTETA GARCIA wrote: >>> Hi Wolfgang and list, >>> >>> Is it possible to do vsn() or justvsn() with >>> backgroundSubtract=TRUE for a one-color genepix chip? I tried and >>> received an error saying that "object R was not found". Could I >>> fool the function duplicating G and Gb into R and Rb or will the >>> normalisation result then be modified and get erroneous output?? >>> >>> >>> Thanks for your help, >>> >>> >>> David >>> >>> _______________________________________________ >>> 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 > > _______________________________________________ > 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