NCI60: Data of the NCI-60 Cell Lines with Missing Individuals

In GonzalezIgnacio/HandlingMissRows: Handling Missing Individuals in Multi-Omics Data Integration

Description

The NCI60 data contain both transcriptomic and proteomic expression for a collection of 60 cell lines from the National Cancer Institute (NCI-60). Data tables with missing individuals have been generated for illustration purposes.

Usage

data(NCI60)

Format

A list with two components, dataTables and mae:

dataTables contain a list with the following components:

trans

a matrix containing 300 rows and 48 columns. The mRNA transcription levels of the NCI60 cell lines. There are 12 missing individuals.

prote

a matrix containing 162 rows and 52 columns. The protein abundance levels of the NCI60 cell lines. There are 8 missing individuals.

cell.line

a DataFrame of cancer types: colon (CO), renal (RE), ovarian (OV), breast (BR), prostate (PR), lung (LC), central nervous system (CNS), leukemia (LE) and melanoma (ME).

mae contain a 'MultiAssayExperiment' instance from NCI60 data with transcriptome and proteomic experiments as described in dataTables.

Details

The transcriptome data was retrieved directly from the NCI60_4arrays package. This data table contains gene expression profiles generated by the Agilent platform with only few hundreds of genes randomly selected to keep the size of the Bioconductor package small. However, the full dataset is available in Reinhold et al. (2012).

The proteomic data was retrieved directly from the rcellminerData package. Protein abundance levels were available for 162 proteins.

The scripts used to generate this data are contained within the inst/extdata folder of the missRows package.

Source

NCI60_4arrays package.

rcellminerData package.

References

Reinhold W.C., Sunshine M., Liu H., Varma S., Kohn K.W., Morris J., Doroshow J., Pommier Y. (2012). Cellminer: A web-based suite of genomic and pharmacologic tools to explore transcript and drug patterns in the NCI-60 cell line set. Cancer Research, 72(14):3499-511.

The CellMiner project website: http://discover.nci.nih.gov/cellminer

GonzalezIgnacio/HandlingMissRows documentation built on Jan. 17, 2020, 6:29 p.m.