The R package datamicroarray provides a collection of scripts to download, process, and load small-sample, high-dimensional microarray data sets to assess machine learning algorithms and models. For each data set, we include a small set of scripts that automatically download, clean, and save the data set.
Each data set is listed below by the first author on the original paper. The data sets are organized them by category; note that most of the data sets are cancer-related. Click a data set to see its description, a link to the original paper, and additional information.
- Breast Cancer
- Central Nervous System Disorders
- Crohn's Disease
- Colon Cancer
- Glioma
- Huntington's Disease
- Leukemia
- Lung Cancer
- Lymphoma
- Myeloma
- Prostate Cancer
- Sarcoma
- Small Round Blue Cell Tumors
- Miscellaneous
You can install the latest package version by typing the following at the R console:
library(devtools)
install_github('ramhiser/datamicroarray')Note that you need to install the devtools package beforehand.
Once you have installed and loaded the datamicroarray package, you can load a data set with the data command. For example, to load the well-known Alon et al. (1999) Colon Cancer data set, type the following at the R console:
library(datamicroarray)
data('alon', package = 'datamicroarray')After loading the data set, the resulting object is a named list with two elements:
x- the data matrix. The rows are thenobservations, and the columns are thepfeatures.y- a factor vector of lengthnwith the corresponding class labels.
Here is a summary for the Alon et al. (1999) Colon Cancer data set.
> dim(alon$x)
[1] 62 2000
> table(alon$y)
n t
22 40 You can see all of the data sets available along with a brief summary of each with the describe_data helper function. Here it is in action:
> describe_data()
author year n p K Disease
1 alon 1999 62 2000 2 Colon Cancer
2 borovecki 2005 31 22283 2 Huntington's Disease
3 burczynski 2006 127 22283 3 Crohn's Disease
4 chiaretti 2004 111 12625 2 Leukemia
5 chin 2006 118 22215 2 Breast Cancer
6 chowdary 2006 104 22283 2 Breast Cancer
7 christensen 2009 217 1413 3 N/A
8 golub 1999 72 7129 3 Leukemia
9 gordon 2002 181 12533 2 Lung Cancer
10 gravier 2010 168 2905 2 Breast Cancer
11 khan 2001 63 2308 4 SRBCT
12 pomeroy 2002 60 7128 2 CNS Tumor
13 shipp 2002 58 6817 2 Lymphoma
14 singh 2002 102 12600 2 Prostate Cancer
15 sorlie 2001 85 456 5 Breast Cancer
16 su 2002 102 5565 4 N/A
17 subramanian 2005 50 10100 2 N/A
18 tian 2003 173 12625 2 Myeloma
19 west 2001 49 7129 2 Breast Cancer
20 yeoh 2002 248 12625 6 Leukemia