Comments (4)
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
.
from plier.
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.
from plier.
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)
from plier.
Thanks now is working!
from plier.
Related Issues (16)
- Q-value error HOT 3
- rseed argument gives "error in Z %*% B : non-conformable arguments" HOT 2
- Adding Release Tag HOT 6
- Issue while running Tutorial HOT 8
- Prior data HOT 6
- Recommendation on the size of prior data? HOT 3
- Several questions about PLIER HOT 4
- Does these errors occur due to the small size of my dataset? HOT 2
- making a new pathways matrix HOT 14
- description of the outputs of PLIER() function HOT 4
- Problem with installing Rd object HOT 1
- Two question regarding interpretation of the pathways having significant AUC for a specific LV HOT 1
- Should the input gene expression data be log scale or not? HOT 2
- try to apply PLIER to seurat object: Error in qr.default(Y, complete = FALSE) : NA/NaN/Inf in foreign function call (arg 1) HOT 1
- Can the data of mRNA of human tissue be use this method? HOT 8
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