[BioC] Reference Normalization using vsn2

Sam Wong qxsr at yahoo.com
Thu Jul 16 00:49:43 CEST 2009

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) 

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


Sam Wong

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