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?
•
written
by
aishwaryamandava7 •
2 answers
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.
You can download the data at CellMiner.
Log in to answer this question.
-
Sample clustering from 10X single cell
written by synat.keam •
-
How to normalize NCI-60 gene expression data
written by hAjmal •
-
median probe intensity does not correlate with RNA-seq data - what's the best practice to compare t…
written by CrazyB
-
Help with creating tumor cell line network
written by torgeirous •
-
Determining Up and Down regulated genes from GEO GDS4296
written by hAjmal •
-
Where to find gene expression data with different drug on the NCI 60?
written by zero_hsy
-
What is the difference between RNA: Affy HG-U95(A-E), RNA: Affy HG-U133(A-B), RNA: Affy HG-U133 Plu…
written by zero_hsy
-
Where can I download the NCI 60 data(gene expression,micRNA,protein data)
written by zero_hsy
-
Where can I download NCI 60 data?
written by zero_hsy
-
Rna-Sequencing For Nci-60 Data
written by pm2013 •
