Dear List; I am trying to normalize a matrix using vsn2 and a reference set. Here are my syntax and the error message I received: > ref<-vsn2(raw.mat2[1:67,],lts.quantile=1) vsn2: 67 x 316 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. > > raw.vsn2<-vsn2(raw.mat2[68:888,],reference=ref) Error in .local(x, reference, strata, ...) : 'nrow(reference)' must be equal to 'nrow(x)'. > > traceback() 6: stop("'nrow(reference)' must be equal to 'nrow(x)'.") 5: .local(x, reference, strata, ...) 4: is(object, Cl) 3: is(object, Cl) 2: .valueClassTest(standardGeneric("vsn2"), "vsn", "vsn2") 1: vsn2(raw.mat2[68:888, ], reference = ref) > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] vsn_3.12.0 Biobase_2.4.1 loaded via a namespace (and not attached): [1] affy_1.22.0 affyio_1.12.0 grid_2.9.0 lattice_0.17-22 limma_2.18.0 [6] preprocessCore_1.6.0 ROC_1.18.0 tools_2.9.0 > The original data is in raw.mat2 which is 888 x 316. The reference is the first 67 rows and the rest of the data matrix (rows 68 to 888) is to be normalized to the reference set. I wonder what could possibly cause the error? Any help would be appreciated Thanks Sam Wong

Dear Sam Please have a look at the vsn vignette (Introduction to vsn, [1]). What you want to do, I think, is described in Section 7 (Normalisation with 'spike-in' probes). The syntax you are using would apply to a different problem, described in Section 8. [1] http://www.bioconductor.org/packages/2.5/bioc/html/vsn.html Best wishes Wolfgang Wong wrote: > > Dear List; > > I am trying to normalize a matrix using vsn2 and a reference set. Here are my syntax and the error message I received: > >> ref<-vsn2(raw.mat2[1:67,],lts.quantile=1) > vsn2: 67 x 316 matrix (1 stratum). > Please use 'meanSdPlot' to verify the fit. >> raw.vsn2<-vsn2(raw.mat2[68:888,],reference=ref) > Error in .local(x, reference, strata, ...) : > 'nrow(reference)' must be equal to 'nrow(x)'. >> traceback() > 6: stop("'nrow(reference)' must be equal to 'nrow(x)'.") > 5: .local(x, reference, strata, ...) > 4: is(object, Cl) > 3: is(object, Cl) > 2: .valueClassTest(standardGeneric("vsn2"), "vsn", "vsn2") > 1: vsn2(raw.mat2[68:888, ], reference = ref) >> sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] vsn_3.12.0 Biobase_2.4.1 > > loaded via a namespace (and not attached): > [1] affy_1.22.0 affyio_1.12.0 grid_2.9.0 lattice_0.17-22 limma_2.18.0 > [6] preprocessCore_1.6.0 ROC_1.18.0 tools_2.9.0 > > The original data is in raw.mat2 which is 888 x 316. The reference is the first 67 rows and the rest of the data matrix (rows 68 to 888) is to be normalized to the reference set. I wonder what could possibly cause the error? > > Any help would be appreciated > > Thanks > > Sam Wong > > _______________________________________________ > 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