PLIER::num.pc error

[msubirana]

I want to define the principle components for defining the range of k, but I got this error:

k <- PLIER::num.pc(data=gtex_expression_matrix_cm)
Error in if ((class(data) != "list") & (class(data) != "rsvd")) { : 
  the condition has length > 1

The gtex_expression_matrix_cm is the same object used i PLIER::PLIER and works perfectly.

[wgmao]

Thank you for your interest in the package. If you run class(gtex_expression_matrix_cm), you should see multiple values which leads to this error. One workaround is to use as.matrix(gtex_expression_matrix_cm) as input for num.pc.

[msubirana]

gtex_expression_matrix_cm is already a matrix. If I use as.matrix(gtex_expression_matrix_cm) as input for num.pc, I encounter the same error.

[wgmao]

It should be easily solvable if I know more about the data. Without seeing the data, I would suggest to use the following code block.

rowNorm=function(x){
  s=apply(x,1,sd)
  m=apply(x,1,mean);
  x=sweep(x,1,m)
  x=sweep(x,1,s,"/")
  x
}

ng=nrow(gtex_expression_matrix_cm)
ns=ncol(gtex_expression_matrix_cm)
Y = rowNorm(gtex_expression_matrix_cm)

if (ns > 500){
svdres=rsvd::rsvd(Y, k=min(ns, max(200, ns/4)), q=3)
}else{
svdres=svd(Y)
}#else
#Then call num.pc(svdres)

[msubirana]

Thanks now is working!