[BioC] Reference Normalization using vsn2
qxsr at yahoo.com
Thu Jul 16 00:49:43 CEST 2009
I am trying to normalize a matrix using vsn2 and a reference set. Here are my syntax and the error message I received:
vsn2: 67 x 316 matrix (1 stratum).
Please use 'meanSdPlot' to verify the fit.
Error in .local(x, reference, strata, ...) :
'nrow(reference)' must be equal to 'nrow(x)'.
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)
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:
 stats graphics grDevices datasets utils methods base
other attached packages:
 vsn_3.12.0 Biobase_2.4.1
loaded via a namespace (and not attached):
 affy_1.22.0 affyio_1.12.0 grid_2.9.0 lattice_0.17-22 limma_2.18.0
 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
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