NCI-60 dataset in R

Question

[aishwaryamandava7]

I am working on clustering NCI-60 dataset. I am confused whether I should consider using the NCI-60 data from ISLR package or from made4 package. The dataset on ISLR package has 64 cell lines with 6830 genes, while the one from made4 package has 60 cell lines and 1517 gene expression measurements. Is there any other source that I can get the data from?

Answer 1

[cannin]

Use the rcellminer package.

https://bioconductor.org/packages/release/bioc/html/rcellminer.html https://www.ncbi.nlm.nih.gov/pubmed/26635141

Those R scripts that you're about to write if you download the data directly and import have been written (and tested) for you by the CellMiner group and colleagues. The tutorial (vignette) shows you various cases for using the data taken from recent papers.

https://bioconductor.org/packages/release/bioc/vignettes/rcellminer/inst/doc/rcellminerUsage.html

I'm an author on the package and its the only way I use NCI-60 data in R.

[hAjmal]

Hi Canin, Is there a way to download raw read counts of NCI-60 data using Rcellminer?

[cannin]

Not at the moment; you'll need to contact: [e-mail]

Answer 2

[Jean-Karim Heriche]

You can download the data at CellMiner.