[BioC] Reference Normalization using vsn2

[Wolfgang Huber]

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
> 
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