Hi guys,

I tried to use SVA package to identify number of batch factors in my gene expression dataset. But I ran into an error message:

> library(sva)
> load("myeset.RData")
> pheno <- pData(myeset)
> str(pheno)
'data.frame':   821 obs. of  4 variables:
$ sample    : Factor w/ 821 levels "A_837766__U133Plus2",..: 1 2 3 4 5 6 7 8 9 10 ...
$ Source    : Factor w/ 6 levels "C1","C2",..: 5 5 5 5 5 5 5 5 5 5 ...
$ CancerType: Factor w/ 28 levels "Anus","Bladder",..: 10 14 14 10 10 14 14 14 11 14 ...
$ Batch     : Factor w/ 14 levels "20110909_U133Plus2",..: 1 1 1 1 1 1 1 1 1 1 ...
> edata <- exprs(myeset)
> str(edata)
num [1:18960, 1:821] 4.98 4.95 8.29 4.21 2.9 ...
- attr(*, "dimnames")=List of 2
  ..$ : chr [1:18960] "100009676_at" "10000_at" "10001_at" "10002_at" ...
  ..$ : chr [1:821] "A_837766__U133Plus2" "A_937608__U133Plus2" "A_949340__U133Plus2" "A_949363__U133Plus2" ...
>
> mod <- model.matrix(~as.factor(CancerType), data=pheno)
> mod0 ~ model.matrix(~1,data=pheno)
mod0 ~ model.matrix(~1, data = pheno)
> n.sv = num.sv(edata,mod,method="leek")
Error in diag(dims[2]) - mod %*% solve(t(mod) %*% mod) %*% t(mod) :
  non-conformable arrays


Any suggestion?

Thanks a lot,

Ying

> traceback()
1: num.sv(edata, mod, method = "leek")
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252

attached base packages:
[1] splines   parallel  stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] pamr_1.54.1        survival_2.37-4    cluster_1.14.4     bladderbatch_1.0.5 sva_3.6.0          mgcv_1.7-24        corpcor_1.6.6
[8] Biobase_2.20.1     BiocGenerics_0.6.0

loaded via a namespace (and not attached):
[1] grid_3.0.1      lattice_0.20-15 Matrix_1.0-12   nlme_3.1-110    tools_3.0.1
>
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