We read every piece of feedback, and take your input very seriously.
To see all available qualifiers, see our documentation.
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
I have installed scPred and been following the article Intro and executed this code
library("scPred") library("tidyverse") download.file("https://scrnaseq-public-datasets.s3.amazonaws.com/scater-objects/pollen.rds", destfile = "~/Downloads/pollen.rds") require("SingleCellExperiment") pollen <- readRDS("~/Downloads/pollen.rds") pollen_counts <- normcounts(pollen) pollen_cpm <- apply(pollen_counts, 2, function(x) (x/sum(x))*1000000) pollen_metadata <- as.data.frame(colData(pollen)) set.seed(1234) i <- createDataPartition(pollen_metadata$cell_type2, p = 0.70, list = FALSE) train_data <- pollen_cpm[, i] test_data <- pollen_cpm[, -i] train_info <- pollen_metadata[i, , drop = FALSE] test_info <- pollen_metadata[-i, , drop = FALSE] set.seed(1234) scp <- eigenDecompose(train_data, n = 20) scPred::metadata(scp) <- train_info scp <- getFeatureSpace(scp, pVar = "cell_type2") plotEigen(scp, group = "cell_type2") scp <- trainModel(scp, seed = 66)
Then the results I obtained are different from the ones mentioned in the article, I get the following AUC scores
Training information Model: Support Vector Machines with Class Weights AUC Precision Recall F blood 0.938 1 0.988 0.994 dermal 0.929 1 1 1 neural 0.891 1 0.869 0.926 pluripotent 0.7 1 1 1
The text was updated successfully, but these errors were encountered:
No branches or pull requests
I have installed scPred and been following the article Intro and executed this code
Then the results I obtained are different from the ones mentioned in the article, I get the following AUC scores
The text was updated successfully, but these errors were encountered: