sample_data_extern {RobustPrediction} | R Documentation |
Sample External Validation Data Subset
Description
This dataset, named 'sample_data_extern', is a subset of publicly available microarray data from the HG-U133PLUS2 chip. It contains expression levels of 200 genes across 50 samples, used primarily as an external validation set in robust feature selection studies. The data has been sourced from the ArrayExpress repository and has been referenced in several research articles.
Usage
sample_data_extern
Format
A data frame with 50 observations and 201 variables, including:
- y
Factor. The response variable.
- 236694_at
Numeric. Expression level of gene 236694_at.
- 222356_at
Numeric. Expression level of gene 222356_at.
- 1554125_a_at
Numeric. Expression level of gene 1554125_a_at.
- 232823_at
Numeric. Expression level of gene 232823_at.
- 205766_at
Numeric. Expression level of gene 205766_at.
- 1560446_at
Numeric. Expression level of gene 1560446_at.
- 202565_s_at
Numeric. Expression level of gene 202565_s_at.
- 234887_at
Numeric. Expression level of gene 234887_at.
- 209687_at
Numeric. Expression level of gene 209687_at.
- 221592_at
Numeric. Expression level of gene 221592_at.
- 1570123_at
Numeric. Expression level of gene 1570123_at.
- 241368_at
Numeric. Expression level of gene 241368_at.
- 243324_x_at
Numeric. Expression level of gene 243324_x_at.
- 224046_s_at
Numeric. Expression level of gene 224046_s_at.
- 202775_s_at
Numeric. Expression level of gene 202775_s_at.
- 216332_at
Numeric. Expression level of gene 216332_at.
- 1569545_at
Numeric. Expression level of gene 1569545_at.
- 205946_at
Numeric. Expression level of gene 205946_at.
- 203547_at
Numeric. Expression level of gene 203547_at.
- 243239_at
Numeric. Expression level of gene 243239_at.
- 234245_at
Numeric. Expression level of gene 234245_at.
- 210832_x_at
Numeric. Expression level of gene 210832_x_at.
- 224549_x_at
Numeric. Expression level of gene 224549_x_at.
- 236628_at
Numeric. Expression level of gene 236628_at.
- 214848_at
Numeric. Expression level of gene 214848_at.
- 1553015_a_at
Numeric. Expression level of gene 1553015_a_at.
- 1554199_at
Numeric. Expression level of gene 1554199_at.
- 1557636_a_at
Numeric. Expression level of gene 1557636_a_at.
- 1558511_s_at
Numeric. Expression level of gene 1558511_s_at.
- 1561713_at
Numeric. Expression level of gene 1561713_at.
- 1561883_at
Numeric. Expression level of gene 1561883_at.
- 1568720_at
Numeric. Expression level of gene 1568720_at.
- 1569168_at
Numeric. Expression level of gene 1569168_at.
- 1569443_s_at
Numeric. Expression level of gene 1569443_s_at.
- 1570103_at
Numeric. Expression level of gene 1570103_at.
- 200916_at
Numeric. Expression level of gene 200916_at.
- 201554_x_at
Numeric. Expression level of gene 201554_x_at.
- 202371_at
Numeric. Expression level of gene 202371_at.
- 204481_at
Numeric. Expression level of gene 204481_at.
- 205831_at
Numeric. Expression level of gene 205831_at.
- 207061_at
Numeric. Expression level of gene 207061_at.
- 207423_s_at
Numeric. Expression level of gene 207423_s_at.
- 209896_s_at
Numeric. Expression level of gene 209896_s_at.
- 212646_at
Numeric. Expression level of gene 212646_at.
- 214068_at
Numeric. Expression level of gene 214068_at.
- 217727_x_at
Numeric. Expression level of gene 217727_x_at.
- 221103_s_at
Numeric. Expression level of gene 221103_s_at.
- 221785_at
Numeric. Expression level of gene 221785_at.
- 224207_x_at
Numeric. Expression level of gene 224207_x_at.
- 228257_at
Numeric. Expression level of gene 228257_at.
- 228877_at
Numeric. Expression level of gene 228877_at.
- 231173_at
Numeric. Expression level of gene 231173_at.
- 231328_s_at
Numeric. Expression level of gene 231328_s_at.
- 231639_at
Numeric. Expression level of gene 231639_at.
- 232221_x_at
Numeric. Expression level of gene 232221_x_at.
- 232349_x_at
Numeric. Expression level of gene 232349_x_at.
- 232849_at
Numeric. Expression level of gene 232849_at.
- 233601_at
Numeric. Expression level of gene 233601_at.
- 234403_at
Numeric. Expression level of gene 234403_at.
- 234585_at
Numeric. Expression level of gene 234585_at.
- 234650_at
Numeric. Expression level of gene 234650_at.
- 234897_s_at
Numeric. Expression level of gene 234897_s_at.
- 236071_at
Numeric. Expression level of gene 236071_at.
- 236689_at
Numeric. Expression level of gene 236689_at.
- 238551_at
Numeric. Expression level of gene 238551_at.
- 239414_at
Numeric. Expression level of gene 239414_at.
- 241034_at
Numeric. Expression level of gene 241034_at.
- 241131_at
Numeric. Expression level of gene 241131_at.
- 241897_at
Numeric. Expression level of gene 241897_at.
- 242611_at
Numeric. Expression level of gene 242611_at.
- 244805_at
Numeric. Expression level of gene 244805_at.
- 244866_at
Numeric. Expression level of gene 244866_at.
- 32259_at
Numeric. Expression level of gene 32259_at.
- 1552264_a_at
Numeric. Expression level of gene 1552264_a_at.
- 1552880_at
Numeric. Expression level of gene 1552880_at.
- 1553186_x_at
Numeric. Expression level of gene 1553186_x_at.
- 1553372_at
Numeric. Expression level of gene 1553372_at.
- 1553438_at
Numeric. Expression level of gene 1553438_at.
- 1554299_at
Numeric. Expression level of gene 1554299_at.
- 1554362_at
Numeric. Expression level of gene 1554362_at.
- 1554491_a_at
Numeric. Expression level of gene 1554491_a_at.
- 1555098_a_at
Numeric. Expression level of gene 1555098_a_at.
- 1555990_at
Numeric. Expression level of gene 1555990_at.
- 1556034_s_at
Numeric. Expression level of gene 1556034_s_at.
- 1556822_s_at
Numeric. Expression level of gene 1556822_s_at.
- 1556824_at
Numeric. Expression level of gene 1556824_at.
- 1557278_s_at
Numeric. Expression level of gene 1557278_s_at.
- 1558603_at
Numeric. Expression level of gene 1558603_at.
- 1558890_at
Numeric. Expression level of gene 1558890_at.
- 1560791_at
Numeric. Expression level of gene 1560791_at.
- 1561083_at
Numeric. Expression level of gene 1561083_at.
- 1561364_at
Numeric. Expression level of gene 1561364_at.
- 1561553_at
Numeric. Expression level of gene 1561553_at.
- 1562523_at
Numeric. Expression level of gene 1562523_at.
- 1562613_at
Numeric. Expression level of gene 1562613_at.
- 1563351_at
Numeric. Expression level of gene 1563351_at.
- 1563473_at
Numeric. Expression level of gene 1563473_at.
- 1566780_at
Numeric. Expression level of gene 1566780_at.
- 1567257_at
Numeric. Expression level of gene 1567257_at.
- 1569664_at
Numeric. Expression level of gene 1569664_at.
- 1569882_at
Numeric. Expression level of gene 1569882_at.
- 1570252_at
Numeric. Expression level of gene 1570252_at.
- 201089_at
Numeric. Expression level of gene 201089_at.
- 201261_x_at
Numeric. Expression level of gene 201261_x_at.
- 202052_s_at
Numeric. Expression level of gene 202052_s_at.
- 202236_s_at
Numeric. Expression level of gene 202236_s_at.
- 202948_at
Numeric. Expression level of gene 202948_at.
- 203080_s_at
Numeric. Expression level of gene 203080_s_at.
- 203211_s_at
Numeric. Expression level of gene 203211_s_at.
- 203218_at
Numeric. Expression level of gene 203218_at.
- 203236_s_at
Numeric. Expression level of gene 203236_s_at.
- 203347_s_at
Numeric. Expression level of gene 203347_s_at.
- 203960_s_at
Numeric. Expression level of gene 203960_s_at.
- 204609_at
Numeric. Expression level of gene 204609_at.
- 204806_x_at
Numeric. Expression level of gene 204806_x_at.
- 204949_at
Numeric. Expression level of gene 204949_at.
- 204979_s_at
Numeric. Expression level of gene 204979_s_at.
- 205823_at
Numeric. Expression level of gene 205823_at.
- 205902_at
Numeric. Expression level of gene 205902_at.
- 205967_at
Numeric. Expression level of gene 205967_at.
- 206186_at
Numeric. Expression level of gene 206186_at.
- 207151_at
Numeric. Expression level of gene 207151_at.
- 207379_at
Numeric. Expression level of gene 207379_at.
- 207440_at
Numeric. Expression level of gene 207440_at.
- 207883_s_at
Numeric. Expression level of gene 207883_s_at.
- 208277_at
Numeric. Expression level of gene 208277_at.
- 208280_at
Numeric. Expression level of gene 208280_at.
- 209224_s_at
Numeric. Expression level of gene 209224_s_at.
- 209561_at
Numeric. Expression level of gene 209561_at.
- 209630_s_at
Numeric. Expression level of gene 209630_s_at.
- 210118_s_at
Numeric. Expression level of gene 210118_s_at.
- 210342_s_at
Numeric. Expression level of gene 210342_s_at.
- 211566_x_at
Numeric. Expression level of gene 211566_x_at.
- 211756_at
Numeric. Expression level of gene 211756_at.
- 212170_at
Numeric. Expression level of gene 212170_at.
- 212494_at
Numeric. Expression level of gene 212494_at.
- 213118_at
Numeric. Expression level of gene 213118_at.
- 214475_x_at
Numeric. Expression level of gene 214475_x_at.
- 214834_at
Numeric. Expression level of gene 214834_at.
- 215718_s_at
Numeric. Expression level of gene 215718_s_at.
- 216283_s_at
Numeric. Expression level of gene 216283_s_at.
- 217206_at
Numeric. Expression level of gene 217206_at.
- 217557_s_at
Numeric. Expression level of gene 217557_s_at.
- 217577_at
Numeric. Expression level of gene 217577_at.
- 218152_at
Numeric. Expression level of gene 218152_at.
- 218252_at
Numeric. Expression level of gene 218252_at.
- 219714_s_at
Numeric. Expression level of gene 219714_s_at.
- 220506_at
Numeric. Expression level of gene 220506_at.
- 220889_s_at
Numeric. Expression level of gene 220889_s_at.
- 221204_s_at
Numeric. Expression level of gene 221204_s_at.
- 221795_at
Numeric. Expression level of gene 221795_at.
- 222048_at
Numeric. Expression level of gene 222048_at.
- 223142_s_at
Numeric. Expression level of gene 223142_s_at.
- 223439_at
Numeric. Expression level of gene 223439_at.
- 223673_at
Numeric. Expression level of gene 223673_at.
- 224363_at
Numeric. Expression level of gene 224363_at.
- 224512_s_at
Numeric. Expression level of gene 224512_s_at.
- 224690_at
Numeric. Expression level of gene 224690_at.
- 224936_at
Numeric. Expression level of gene 224936_at.
- 225334_at
Numeric. Expression level of gene 225334_at.
- 225713_at
Numeric. Expression level of gene 225713_at.
- 225839_at
Numeric. Expression level of gene 225839_at.
- 226041_at
Numeric. Expression level of gene 226041_at.
- 226093_at
Numeric. Expression level of gene 226093_at.
- 226543_at
Numeric. Expression level of gene 226543_at.
- 227695_at
Numeric. Expression level of gene 227695_at.
- 228295_at
Numeric. Expression level of gene 228295_at.
- 228548_at
Numeric. Expression level of gene 228548_at.
- 229234_at
Numeric. Expression level of gene 229234_at.
- 229658_at
Numeric. Expression level of gene 229658_at.
- 229725_at
Numeric. Expression level of gene 229725_at.
- 230252_at
Numeric. Expression level of gene 230252_at.
- 230471_at
Numeric. Expression level of gene 230471_at.
- 231149_s_at
Numeric. Expression level of gene 231149_s_at.
- 231556_at
Numeric. Expression level of gene 231556_at.
- 231754_at
Numeric. Expression level of gene 231754_at.
- 232011_s_at
Numeric. Expression level of gene 232011_s_at.
- 233030_at
Numeric. Expression level of gene 233030_at.
- 234161_at
Numeric. Expression level of gene 234161_at.
- 235050_at
Numeric. Expression level of gene 235050_at.
- 235094_at
Numeric. Expression level of gene 235094_at.
- 235278_at
Numeric. Expression level of gene 235278_at.
- 235671_at
Numeric. Expression level of gene 235671_at.
- 235952_at
Numeric. Expression level of gene 235952_at.
- 236158_at
Numeric. Expression level of gene 236158_at.
- 236181_at
Numeric. Expression level of gene 236181_at.
- 237055_at
Numeric. Expression level of gene 237055_at.
- 237768_x_at
Numeric. Expression level of gene 237768_x_at.
- 238897_at
Numeric. Expression level of gene 238897_at.
- 239160_at
Numeric. Expression level of gene 239160_at.
- 239998_at
Numeric. Expression level of gene 239998_at.
- 240254_at
Numeric. Expression level of gene 240254_at.
- 240612_at
Numeric. Expression level of gene 240612_at.
- 240692_at
Numeric. Expression level of gene 240692_at.
- 240822_at
Numeric. Expression level of gene 240822_at.
- 240842_at
Numeric. Expression level of gene 240842_at.
- 241331_at
Numeric. Expression level of gene 241331_at.
- 241598_at
Numeric. Expression level of gene 241598_at.
- 241927_x_at
Numeric. Expression level of gene 241927_x_at.
- 242405_at
Numeric. Expression level of gene 242405_at.
Details
This dataset was extracted from a larger dataset available on ArrayExpress and is used as an external validation set for feature selection tasks and other machine learning applications in bioinformatics.
Source
The original dataset can be found on ArrayExpress: https://www.ebi.ac.uk/arrayexpress
References
Ellenbach, N., Boulesteix, A.L., Bischl, B., et al. (2021). Improved Outcome Prediction Across Data Sources Through Robust Parameter Tuning. Journal of Classification, 38, 212–231. doi:10.1007/s00357-020-09368-z.
Hornung, R., Causeur, D., Bernau, C., Boulesteix, A.L. (2017). Improving cross-study prediction through addon batch effect adjustment or addon normalization. Bioinformatics, 33(3), 397–404. doi:10.1093/bioinformatics/btw650.
Examples
# Load the dataset
data(sample_data_extern)
# View the first few rows of the dataset
head(sample_data_extern)
# Summary of the dataset
summary(sample_data_extern)