colon: Colon Cancer Dataset

Description Usage Format Source References Examples

Description

The dataset describes a colon cancer study (Alon et al., 1999) in which gene expression levels were measured on 40 normal tissues and on 22 tumor colon tissues. Note that a logarithmic (base 10) transformation has been applied to the gene expression levels.

Usage

1

Format

A data frame in which the rows correspond to 2000 genes and the columns to 62 tissues. The first 40 columns belong to the normal tissue group while the last 22 columns to the tumor colon tissue group.

Source

http://genomics-pubs.princeton.edu/oncology/affydata [Last Assessed: 2016-05-21]

References

Alon, U., Barkai, N., Notterman, D.A., Gish, K., Ybarra, S., Mack, D. and Levine, A.J. (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proceedings of the National Academy of Sciences of the United States of America 96, 6745–6750.

Examples

1
2

Example output

    normal.1         normal.2         normal.3         normal.4     
 Min.   :0.8689   Min.   :0.7793   Min.   :0.8041   Min.   :0.8201  
 1st Qu.:1.9485   1st Qu.:1.7123   1st Qu.:1.8690   1st Qu.:1.9282  
 Median :2.2302   Median :2.0215   Median :2.1241   Median :2.1848  
 Mean   :2.2568   Mean   :2.0441   Mean   :2.1702   Mean   :2.2261  
 3rd Qu.:2.5125   3rd Qu.:2.3442   3rd Qu.:2.4341   3rd Qu.:2.4758  
 Max.   :3.9340   Max.   :4.2590   Max.   :3.6474   Max.   :3.8529  
    normal.5        normal.6        normal.7         normal.8     
 Min.   :0.833   Min.   :1.001   Min.   :0.8897   Min.   :0.8988  
 1st Qu.:2.019   1st Qu.:2.248   1st Qu.:1.9726   1st Qu.:2.0366  
 Median :2.327   Median :2.577   Median :2.2119   Median :2.3043  
 Mean   :2.354   Mean   :2.586   Mean   :2.2554   Mean   :2.3450  
 3rd Qu.:2.680   3rd Qu.:2.910   3rd Qu.:2.4987   3rd Qu.:2.6039  
 Max.   :4.030   Max.   :4.172   Max.   :3.7132   Max.   :3.8084  
    normal.9        normal.10        normal.11        normal.12    
 Min.   :0.7745   Min.   :0.7782   Min.   :0.9988   Min.   :0.805  
 1st Qu.:1.6375   1st Qu.:1.8067   1st Qu.:2.0585   1st Qu.:1.641  
 Median :1.9352   Median :2.0947   Median :2.3141   Median :1.967  
 Mean   :1.9805   Mean   :2.1274   Mean   :2.3549   Mean   :2.023  
 3rd Qu.:2.2789   3rd Qu.:2.4068   3rd Qu.:2.6366   3rd Qu.:2.342  
 Max.   :3.8540   Max.   :3.7310   Max.   :3.9547   Max.   :4.083  
   normal.13       normal.14       normal.15        normal.16    
 Min.   :0.770   Min.   :1.156   Min.   :0.9927   Min.   :1.072  
 1st Qu.:2.075   1st Qu.:1.907   1st Qu.:1.9216   1st Qu.:2.182  
 Median :2.336   Median :2.177   Median :2.1802   Median :2.450  
 Mean   :2.381   Mean   :2.212   Mean   :2.2187   Mean   :2.487  
 3rd Qu.:2.658   3rd Qu.:2.472   3rd Qu.:2.4636   3rd Qu.:2.728  
 Max.   :3.973   Max.   :3.773   Max.   :3.7650   Max.   :3.991  
   normal.17        normal.18       normal.19       normal.20     
 Min.   :0.9859   Min.   :1.052   Min.   :1.109   Min.   :0.8108  
 1st Qu.:2.3015   1st Qu.:2.258   1st Qu.:2.252   1st Qu.:1.8946  
 Median :2.5680   Median :2.531   Median :2.519   Median :2.2044  
 Mean   :2.5917   Mean   :2.561   Mean   :2.555   Mean   :2.2159  
 3rd Qu.:2.8640   3rd Qu.:2.812   3rd Qu.:2.809   3rd Qu.:2.5131  
 Max.   :4.1247   Max.   :4.113   Max.   :4.090   Max.   :3.7000  
   normal.21        normal.22       normal.23       normal.24    
 Min.   :0.9599   Min.   :1.098   Min.   :1.009   Min.   :0.784  
 1st Qu.:1.8735   1st Qu.:2.180   1st Qu.:1.924   1st Qu.:1.882  
 Median :2.1623   Median :2.431   Median :2.193   Median :2.164  
 Mean   :2.2007   Mean   :2.472   Mean   :2.234   Mean   :2.207  
 3rd Qu.:2.4842   3rd Qu.:2.716   3rd Qu.:2.510   3rd Qu.:2.499  
 Max.   :3.8392   Max.   :4.102   Max.   :3.708   Max.   :3.717  
   normal.25        normal.26        normal.27        normal.28     
 Min.   :0.7868   Min.   :0.8317   Min.   :0.9149   Min.   :0.7734  
 1st Qu.:2.1268   1st Qu.:1.8344   1st Qu.:2.0555   1st Qu.:1.7486  
 Median :2.4105   Median :2.1342   Median :2.3128   Median :2.0617  
 Mean   :2.4257   Mean   :2.1772   Mean   :2.3375   Mean   :2.0940  
 3rd Qu.:2.7249   3rd Qu.:2.4809   3rd Qu.:2.5960   3rd Qu.:2.4062  
 Max.   :4.0066   Max.   :3.8310   Max.   :3.9604   Max.   :3.7533  
   normal.29       normal.30       normal.31        normal.32    
 Min.   :1.194   Min.   :1.626   Min.   :0.9607   Min.   :1.186  
 1st Qu.:2.298   1st Qu.:2.426   1st Qu.:2.3455   1st Qu.:2.324  
 Median :2.593   Median :2.686   Median :2.6237   Median :2.613  
 Mean   :2.613   Mean   :2.709   Mean   :2.6468   Mean   :2.641  
 3rd Qu.:2.895   3rd Qu.:2.935   3rd Qu.:2.9036   3rd Qu.:2.940  
 Max.   :4.166   Max.   :4.038   Max.   :4.1574   Max.   :4.005  
   normal.33        normal.34       normal.35        normal.36    
 Min.   :0.8886   Min.   :1.299   Min.   :0.8776   Min.   :0.811  
 1st Qu.:1.9668   1st Qu.:2.216   1st Qu.:1.9655   1st Qu.:1.958  
 Median :2.2423   Median :2.501   Median :2.2529   Median :2.228  
 Mean   :2.2659   Mean   :2.542   Mean   :2.2891   Mean   :2.256  
 3rd Qu.:2.5251   3rd Qu.:2.831   3rd Qu.:2.5752   3rd Qu.:2.523  
 Max.   :3.8033   Max.   :4.081   Max.   :3.8846   Max.   :3.656  
   normal.37       normal.38        normal.39        normal.40     
 Min.   :0.799   Min.   :0.7965   Min.   :0.8073   Min.   :0.7831  
 1st Qu.:1.890   1st Qu.:1.6969   1st Qu.:2.0320   1st Qu.:1.9312  
 Median :2.214   Median :2.0179   Median :2.3146   Median :2.2163  
 Mean   :2.231   Mean   :2.0357   Mean   :2.3490   Mean   :2.2330  
 3rd Qu.:2.561   3rd Qu.:2.3411   3rd Qu.:2.6477   3rd Qu.:2.4940  
 Max.   :4.320   Max.   :3.8037   Max.   :4.0501   Max.   :3.7948  
    colon.1         colon.2          colon.3          colon.4      
 Min.   :1.225   Min.   :0.7727   Min.   :0.7693   Min.   :0.7833  
 1st Qu.:2.097   1st Qu.:1.8679   1st Qu.:1.7011   1st Qu.:1.8935  
 Median :2.378   Median :2.1606   Median :1.9883   Median :2.1701  
 Mean   :2.406   Mean   :2.1902   Mean   :2.0227   Mean   :2.2015  
 3rd Qu.:2.669   3rd Qu.:2.4768   3rd Qu.:2.3098   3rd Qu.:2.4758  
 Max.   :3.962   Max.   :3.9312   Max.   :3.5988   Max.   :3.8068  
    colon.5         colon.6         colon.7          colon.8      
 Min.   :1.090   Min.   :1.075   Min.   :0.8452   Min.   :0.7789  
 1st Qu.:2.048   1st Qu.:2.150   1st Qu.:1.8252   1st Qu.:1.6955  
 Median :2.333   Median :2.441   Median :2.0984   Median :2.0258  
 Mean   :2.371   Mean   :2.472   Mean   :2.1438   Mean   :2.0692  
 3rd Qu.:2.658   3rd Qu.:2.737   3rd Qu.:2.4073   3rd Qu.:2.3706  
 Max.   :3.948   Max.   :4.151   Max.   :3.8705   Max.   :3.9252  
    colon.9          colon.10         colon.11        colon.12     
 Min.   :0.7758   Min.   :0.7967   Min.   :1.187   Min.   :0.7666  
 1st Qu.:1.6205   1st Qu.:1.8179   1st Qu.:2.162   1st Qu.:1.3405  
 Median :1.9164   Median :2.1105   Median :2.412   Median :1.6034  
 Mean   :1.9632   Mean   :2.1397   Mean   :2.443   Mean   :1.6625  
 3rd Qu.:2.2613   3rd Qu.:2.4314   3rd Qu.:2.692   3rd Qu.:1.9253  
 Max.   :3.6871   Max.   :3.7246   Max.   :3.947   Max.   :3.3784  
    colon.13         colon.14         colon.15        colon.16    
 Min.   :0.8937   Min.   :0.9112   Min.   :1.090   Min.   :1.002  
 1st Qu.:1.9197   1st Qu.:2.1516   1st Qu.:2.328   1st Qu.:2.214  
 Median :2.1895   Median :2.4005   Median :2.593   Median :2.477  
 Mean   :2.2280   Mean   :2.4352   Mean   :2.620   Mean   :2.499  
 3rd Qu.:2.5116   3rd Qu.:2.6883   3rd Qu.:2.883   3rd Qu.:2.752  
 Max.   :3.7061   Max.   :3.7920   Max.   :4.059   Max.   :3.800  
    colon.17         colon.18        colon.19        colon.20     
 Min.   :0.8979   Min.   :0.859   Min.   :1.063   Min.   :0.7646  
 1st Qu.:2.0669   1st Qu.:1.991   1st Qu.:2.147   1st Qu.:1.9868  
 Median :2.3602   Median :2.277   Median :2.390   Median :2.2637  
 Mean   :2.3952   Mean   :2.306   Mean   :2.423   Mean   :2.2877  
 3rd Qu.:2.6729   3rd Qu.:2.602   3rd Qu.:2.682   3rd Qu.:2.5614  
 Max.   :3.8548   Max.   :3.861   Max.   :3.742   Max.   :4.0152  
    colon.21         colon.22     
 Min.   :0.8711   Min.   :0.9164  
 1st Qu.:2.0611   1st Qu.:2.0259  
 Median :2.3388   Median :2.3095  
 Mean   :2.3591   Mean   :2.3359  
 3rd Qu.:2.6257   3rd Qu.:2.6061  
 Max.   :3.8281   Max.   :3.8734  

ShrinkCovMat documentation built on July 12, 2017, 1:02 a.m.