Description of the dataset

The dataset was published¹ by Kang et al in Plos Computational Biology.

In brief, total mRNA was prepared from Namalwa (Burkitt’s lymphoma), Hs343T (fibroblast line derived from a mammary gland adenocarcinoma), hTERT-HME1 (normal mammary epithelial cells immortalized with hTERT), and MCF7 (estrogen receptor positive breast cancer cell line). mRNA samples were diluted to 100 ng/μl and mixed in different proportions. The mixed RNA samples was profiled by RNA-sequencing. Sequencing libraries were prepared using TruSeq RNA sample preparation kit v2 (Illumina).

Omics_type = tanscriptome

Cancer_type = brca

Cohort_size = 32

Patient_metadata = No

Sample_type = In vitro mixture of cell lines

Preparation of the data

Expression data from array were collected, normalized together using fRMA and transformed using log2.

Normalisation = edgeR

Transformation = Log2 + 1 (pseudo-log2)

Composition of the test dataset

test_data = readRDS("test_data.rds")
length(test_data)

## [1] 1

dim(test_data[[1]])

## [1] 56646    32

colnames(test_data[[1]]) = paste0("sample_",1:dim(test_data[[1]])[2])
knitr::kable(head(test_data[[1]][,1:5], 10))

print(readRDS("input_k_value.rds"))

## [1] 4

print(readRDS("cancer_type.rds"))

## [1] "brca"

Composition of the solution dataset (ground truth)

Source = in vitro mixtures

Number of expected cell types = 4

test_solution = readRDS("test_solution.rds")
length(test_solution)

## [1] 1

dim(test_solution[[1]])

## [1]  4 32