colon: Colon Cancer Dataset
In ShrinkCovMat: Shrinkage Covariance Matrix Estimators
Description
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.
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 # nolint
[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 30, 2019, 9:03 a.m.
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Description 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.
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 # nolint [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
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