[BioC] normalize.AffyBatch.vsn with reference vsn object

[Wolfgang Huber]

Dear Rebecca

thanks. It's been a while since I have seen anyone use this function in 
this mode of use!
I haven't tested this answer, but I suspect that the problem is related 
to the subsampling that vsn2 does by default for AffyBatch objects. What 
happens if in your first call to vsn, you do:

  fit<- vsn2(ab, subsample=0)

Best wishes
	Wolfgang


R Tagett scripsit 05/08/2012 02:33 AM:
> Hello,
> I am trying to normalize an affybatch (U133plus2) against a reference set (all U133plus2) using
> normalize.AffyBatch.vsn(abatch, reference, ...)
> according to the vignette where the reference is a vsn object from a previous fit
> and abatch is an affybatch, but the objects do not seem compatible.
> I hope that you can help.
> A simplified script is shown.
> Thank you,
> Rebecca T
>
>> library(affy)
>> library(vsn)
>> ab<- read.affybatch(filenames= c("GSM467031.CEL.gz","GSM467033.CEL.gz","GSM467035.CEL.gz")   )
>> fit<- vsn2(ab)
> vsn2: 1354896 x 3 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit.
>>
>> # affybatch with one cel in it
>> ab1<- read.affybatch(filenames=c( "GSM467037.CEL.gz"   ))
>
>> normAb<- normalize.AffyBatch.vsn(ab1, reference=fit)
> Error in vsnMatrix(as.matrix(x, ncol = 1), reference, strata, ...) :
>    'nrow(reference)' must be equal to 'nrow(x)'.
>>
>>
>> sessionInfo()
> R version 2.14.0 (2011-10-31)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] hgu133plus2cdf_2.9.1  AnnotationDbi_1.16.19 vsn_3.22.0
> [4] affy_1.32.1           Biobase_2.14.0
>
> loaded via a namespace (and not attached):
>   [1] affyio_1.22.0         BiocInstaller_1.2.1   DBI_0.2-5
>   [4] grid_2.14.0           IRanges_1.12.6        lattice_0.20-6
>   [7] limma_3.10.3          preprocessCore_1.16.0 RSQLite_0.11.1
> [10] tools_2.14.0          zlibbioc_1.0.1
>>
>
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber