| total.data {BNArray} | R Documentation |
Spellman micorarray data set with 6179 genes in 78 experiments to demonstrate BNArray usage.
data(total.data)
The format is: List of 4 $ df.all :`data.frame': 6179 obs. of 78 variables: ..$ V1 : Factor w/ 6179 levels "","YAL001C","YAL002W",..: 1 2 3 4 5 6 7 8 9 10 ... ..$ V2 : Factor w/ 278 levels "","0","-0.01",..: 278 23 11 169 14 86 94 51 37 43 ... ..$ V3 : Factor w/ 277 levels "","0","-0.01",..: 277 1 109 39 168 144 188 32 113 86 ... ..$ V4 : Factor w/ 218 levels "","0","-0.01",..: 218 32 18 15 24 35 41 29 32 26 ... ..$ V5 : Factor w/ 236 levels "","0","-0.01",..: 236 12 36 34 20 94 77 16 77 4 ... ..$ V6 : Factor w/ 334 levels "","0","-0.01",..: 334 31 23 29 5 11 121 57 7 11 ... ..$ V7 : Factor w/ 329 levels "","0","-0.01",..: 329 31 22 143 97 107 91 45 55 28 ... ..$ V8 : Factor w/ 278 levels "","0","-0.01",..: 278 43 4 22 23 95 27 13 36 28 ... ..$ V9 : Factor w/ 266 levels "","0","-0.01",..: 266 36 14 65 26 13 72 46 25 43 ... ..$ V10: Factor w/ 216 levels "","0","-0.01",..: 216 85 10 81 7 24 3 52 55 91 ... ..$ V11: Factor w/ 206 levels "","0","-0.01",..: 206 89 53 117 40 15 100 28 14 43 ... ..$ V12: Factor w/ 215 levels "","0","-0.01",..: 215 31 10 24 28 52 38 70 48 14 ... ..$ V13: Factor w/ 205 levels "","0","-0.01",..: 205 50 40 44 149 94 88 90 24 66 ... ..$ V14: Factor w/ 218 levels "","0","-0.01",..: 218 21 45 20 16 26 47 65 8 2 ... ..$ V15: Factor w/ 209 levels "","0","-0.01",..: 209 1 41 116 10 100 61 54 55 54 ... ..$ V16: Factor w/ 232 levels "","0","-0.01",..: 232 38 26 29 13 85 49 153 49 101 ... ..$ V17: Factor w/ 215 levels "","0","-0.01",..: 215 86 44 60 62 58 48 64 74 64 ... ..$ V18: Factor w/ 190 levels "","0","-0.01",..: 190 51 53 4 95 61 10 19 23 22 ... ..$ V19: Factor w/ 180 levels "","0","-0.01",..: 180 3 61 10 33 37 20 6 2 29 ... ..$ V20: Factor w/ 211 levels "","0","-0.01",..: 211 27 46 12 23 61 38 91 55 143 ... ..$ V21: Factor w/ 177 levels "","0","-0.01",..: 177 151 118 112 48 137 34 96 94 104 ... ..$ V22: Factor w/ 209 levels "","0","-0.01",..: 209 43 73 17 91 49 3 99 48 64 ... ..$ V23: Factor w/ 211 levels "","0","-0.01",..: 211 88 28 68 6 46 43 46 13 28 ... ..$ V24: Factor w/ 356 levels "","0","-0.01",..: 356 33 1 75 1 87 1 41 1 49 ... ..$ V25: Factor w/ 362 levels "","0","-0.01",..: 362 20 1 45 1 264 1 10 5 13 ... ..$ V26: Factor w/ 336 levels "","0","-0.01",..: 336 47 1 33 1 276 1 55 2 23 ... ..$ V27: Factor w/ 313 levels "","0","-0.01",..: 313 8 117 10 264 267 30 81 16 51 ... ..$ V28: Factor w/ 298 levels "","0","-0.01",..: 298 9 48 108 7 75 118 90 30 82 ... ..$ V29: Factor w/ 307 levels "","0","-0.01",..: 307 25 47 51 223 269 52 147 36 105 ... ..$ V30: Factor w/ 311 levels "","0","-0.01",..: 311 57 18 18 13 143 8 8 48 40 ... ..$ V31: Factor w/ 306 levels "","0","-0.01",..: 306 89 125 49 278 261 193 139 40 63 ... ..$ V32: Factor w/ 334 levels "","0","-0.01",..: 334 19 112 76 30 21 2 112 21 128 ... ..$ V33: Factor w/ 302 levels "","0","-0.01",..: 302 26 65 45 216 220 83 107 2 63 ... ..$ V34: Factor w/ 265 levels "","0","-0.01",..: 265 14 8 34 27 67 22 22 43 32 ... ..$ V35: Factor w/ 288 levels "","0","-0.01",..: 288 9 113 43 230 214 30 41 4 55 ... ..$ V36: Factor w/ 277 levels "","0","-0.01",..: 277 64 96 8 55 39 82 60 27 102 ... ..$ V37: Factor w/ 278 levels "","0","-0.01",..: 278 120 31 8 189 169 42 31 241 29 ... ..$ V38: Factor w/ 317 levels "","0","-0.01",..: 317 70 100 98 30 106 50 122 34 94 ... ..$ V39: Factor w/ 279 levels "","0","-0.01",..: 279 57 1 1 1 1 1 1 12 1 ... ..$ V40: Factor w/ 295 levels "","0","-0.01",..: 295 19 48 46 208 227 54 16 60 28 ... ..$ V41: Factor w/ 270 levels "","0","-0.01",..: 270 89 99 13 98 174 79 63 10 113 ... ..$ V42: Factor w/ 296 levels "","0","-0.01",..: 296 64 68 18 293 290 88 62 80 40 ... ..$ V43: Factor w/ 318 levels "","0","-0.01",..: 318 8 38 114 295 316 53 102 43 144 ... ..$ V44: Factor w/ 318 levels "","0","-0.01",..: 318 116 132 98 305 316 67 166 60 148 ... ..$ V45: Factor w/ 338 levels "","0","-0.01",..: 338 2 59 95 245 275 75 17 2 81 ... ..$ V46: Factor w/ 271 levels "","0","-0.01",..: 271 6 1 91 1 235 1 27 2 81 ... ..$ V47: Factor w/ 319 levels "","0","-0.01",..: 319 53 1 83 1 236 1 9 8 105 ... ..$ V48: Factor w/ 378 levels "","0","-0.01",..: 378 39 168 73 311 299 119 232 80 142 ... ..$ V49: Factor w/ 345 levels "","0","-0.01",..: 345 155 3 45 230 294 33 136 175 9 ... ..$ V50: Factor w/ 354 levels "","0","-0.01",..: 354 35 155 46 178 263 134 190 27 67 ... ..$ V51: Factor w/ 299 levels "","0","-0.01",..: 299 39 125 57 15 4 21 1 143 55 ... ..$ V52: Factor w/ 287 levels "","0","-0.01",..: 287 28 30 84 8 108 16 77 42 5 ... ..$ V53: Factor w/ 256 levels "","0","-0.01",..: 256 73 117 161 218 161 67 181 147 171 ... ..$ V54: Factor w/ 267 levels "","0","-0.01",..: 267 111 11 86 16 33 84 11 58 42 ... ..$ V55: Factor w/ 285 levels "","0","-0.01",..: 285 15 48 12 69 123 47 181 52 68 ... ..$ V56: Factor w/ 262 levels "","0","-0.01",..: 262 3 42 95 147 180 103 159 22 32 ... ..$ V57: Factor w/ 363 levels "","0","-0.01",..: 363 8 48 213 37 15 118 106 14 37 ... ..$ V58: Factor w/ 331 levels "","0","-0.01",..: 331 56 18 313 121 192 16 61 38 49 ... ..$ V59: Factor w/ 268 levels "","0","-0.01",..: 268 100 7 78 33 107 66 44 102 7 ... ..$ V60: Factor w/ 242 levels "","0","-0.01",..: 242 172 80 45 25 133 4 8 68 50 ... ..$ V61: Factor w/ 262 levels "","0","-0.01",..: 262 134 19 96 77 1 36 17 14 1 ... ..$ V62: Factor w/ 250 levels "","0","-0.01",..: 250 49 1 176 4 55 1 21 1 24 ... ..$ V63: Factor w/ 289 levels "","0","-0.01",..: 289 8 40 98 1 83 43 1 71 30 ... ..$ V64: Factor w/ 279 levels "","0","-0.01",..: 279 20 29 162 1 72 29 1 90 18 ... ..$ V65: Factor w/ 415 levels "","0","-0.01",..: 415 62 30 308 74 19 35 42 100 136 ... ..$ V66: Factor w/ 273 levels "","0","-0.01",..: 273 25 36 61 22 5 57 82 48 106 ... ..$ V67: Factor w/ 243 levels "","0","-0.01",..: 243 50 8 1 24 1 33 119 14 1 ... ..$ V68: Factor w/ 232 levels "","0","-0.01",..: 232 38 72 80 30 52 42 60 66 101 ... ..$ V69: Factor w/ 254 levels "","0","-0.01",..: 254 49 8 38 31 91 74 85 26 69 ... ..$ V70: Factor w/ 238 levels "","0","-0.01",..: 238 24 17 58 147 167 36 33 26 35 ... ..$ V71: Factor w/ 213 levels "","0","-0.01",..: 213 25 27 32 159 53 80 42 60 76 ... ..$ V72: Factor w/ 183 levels "","0","-0.01",..: 183 76 43 82 41 33 22 16 21 17 ... ..$ V73: Factor w/ 193 levels "","0","-0.01",..: 193 16 13 50 70 62 2 4 83 3 ... ..$ V74: Factor w/ 200 levels "","0","-0.01",..: 200 19 21 46 16 44 33 9 131 6 ... ..$ V75: Factor w/ 198 levels "","0","-0.01",..: 198 65 39 55 119 87 60 5 15 70 ... ..$ V76: Factor w/ 219 levels "","0","-0.01",..: 219 10 18 21 72 44 13 40 71 12 ... ..$ V77: Factor w/ 258 levels "","0","-0.01",..: 258 97 4 70 134 122 53 85 39 187 ... ..$ V78: Factor w/ 182 levels "","0","-0.01",..: 182 10 5 6 66 130 83 60 32 12 ... $ df.ori :`data.frame': 799 obs. of 78 variables: ..$ V1 : Factor w/ 799 levels "YAL022C","YAL040C",..: 1 2 3 4 5 6 7 8 9 10 ... ..$ V2 : num [1:799] -0.22 3.43 0.34 -0.15 0.41 0.77 0.06 -0.25 -0.86 1.17 ... ..$ V3 : num [1:799] -0.86 2.75 0.9 -1.25 0.25 0.8 -1.22 -0.81 -1.03 1.84 ... ..$ V4 : num [1:799] -0.25 0.36 -0.58 NA -0.62 -0.94 -0.76 1.91 3.79 -0.17 ... ..$ V5 : num [1:799] 0.89 0.72 -0.92 0.07 -0.29 -0.42 -0.42 1.82 2.79 -0.94 ... ..$ V6 : num [1:799] -0.36 1.04 0.21 0.01 -0.3 -0.48 -0.35 -0.46 -1.35 -2.06 ... ..$ V7 : num [1:799] -0.42 0.19 -0.2 0.07 -0.45 -0.42 0.1 0.12 -0.86 -1.98 ... ..$ V8 : num [1:799] 0.29 0.47 0.2 0.17 0.75 0.87 0.47 -0.06 -0.22 -1.64 ... ..$ V9 : num [1:799] -0.14 -1.03 0.15 NA 0.37 0.92 0.39 -0.76 -0.38 -0.21 ... ..$ V10: num [1:799] -0.19 -0.63 0.38 -0.1 0.27 0.67 0.17 -0.7 -0.65 1.21 ... ..$ V11: num [1:799] -0.52 -0.68 0.37 0.08 -0.28 -0.18 -0.18 -0.79 -0.79 0.69 ... ..$ V12: num [1:799] 0.04 0.1 0.01 0.64 -0.16 -0.35 -0.21 -0.2 0.02 0.85 ... ..$ V13: num [1:799] 0.04 -0.02 -0.4 0.39 -0.13 -1.06 -0.08 -0.06 0.6 0.43 ... ..$ V14: num [1:799] 0.37 0.53 -0.43 0.33 -0.56 -0.81 -0.36 0.82 1.38 -0.32 ... ..$ V15: num [1:799] 0.24 0.68 -0.62 -0.18 -0.28 -0.18 -0.08 0.36 1.59 -0.77 ... ..$ V16: num [1:799] 0.13 0.51 0.18 -0.54 0.11 0.53 -0.2 0.68 1.03 -1.1 ... ..$ V17: num [1:799] 0.22 -0.2 0.24 -0.2 0.3 0.8 0.5 -0.13 0.99 -0.02 ... ..$ V18: num [1:799] 0.04 -0.34 -0.07 -0.04 0.22 0.45 0.05 0.2 0.11 0.88 ... ..$ V19: num [1:799] -0.24 -0.59 -0.16 -0.54 0.08 0.16 -0.2 -0.32 -0.39 1.3 ... ..$ V20: num [1:799] -0.22 -0.31 0.28 0.29 0.07 -0.09 -0.11 0.04 -0.86 1.29 ... ..$ V21: num [1:799] -0.1 -0.25 0.43 -0.46 -0.02 -0.35 0.3 0.57 -0.41 1.29 ... ..$ V22: num [1:799] 0.22 0.11 -0.21 0.06 0.11 -0.11 -0.21 0.17 -0.2 0.16 ... ..$ V23: num [1:799] 0.61 0.44 -0.33 0.03 -0.1 -0.35 NA 0.53 0.41 0 ... ..$ V24: num [1:799] 0.13 0.49 NA -0.48 NA -0.09 NA 0.23 NA NA ... ..$ V25: num [1:799] -0.24 0.62 NA 0.24 -0.09 0.99 1.02 -0.82 NA -1.32 ... ..$ V26: num [1:799] -0.59 0.05 NA 1.09 0.23 1.53 0.75 -1.2 NA 1.3 ... ..$ V27: num [1:799] -0.57 -0.13 -0.19 1 -0.17 -0.11 -0.65 -1.11 -1.73 0.92 ... ..$ V28: num [1:799] -0.09 0.02 0.52 1.83 -0.17 -0.59 -0.01 -0.04 -0.4 1.72 ... ..$ V29: num [1:799] -0.34 0.04 -0.7 -0.66 -0.44 -1.21 -1.11 -0.16 0.13 -0.61 ... ..$ V30: num [1:799] 0.49 -0.14 -0.25 0.25 -0.59 -1.43 -0.31 0.4 0.47 -0.69 ... ..$ V31: num [1:799] 0.32 0.24 -1.05 -1.1 -0.51 -1.37 -0.88 1.12 1.15 -1.76 ... ..$ V32: num [1:799] 1.15 0.91 0.31 -0.1 -0.23 -1.16 0.22 0.34 1.86 -1.36 ... ..$ V33: num [1:799] 0.2 0.42 -0.19 -0.58 0.36 0.72 -0.11 0.39 0.42 -1.32 ... ..$ V34: num [1:799] 0.31 0.58 0.86 0.04 0.52 0.94 0.58 0.21 0.4 0.26 ... ..$ V35: num [1:799] -0.28 -0.2 0.35 NA 0.67 1.15 0.64 -0.5 -0.85 1.01 ... ..$ V36: num [1:799] -0.01 0.03 0.79 0.99 0.57 0.85 0.43 -0.2 -0.75 0.2 ... ..$ V37: num [1:799] -0.48 -0.38 0.02 -0.48 -0.49 0.99 0.02 -0.7 -1.28 1.45 ... ..$ V38: num [1:799] -0.4 -0.31 0.34 1.05 0.28 0.15 0.12 -1.17 -1.4 1.63 ... ..$ V39: num [1:799] -0.59 -0.56 NA -0.87 -0.15 -0.43 -0.55 NA NA 0.43 ... ..$ V40: num [1:799] 0.54 0.17 0.21 0.58 0.23 -0.66 -0.21 -0.1 -0.09 0.91 ... ..$ V41: num [1:799] -0.09 -0.3 -0.95 -1.18 -0.42 -0.85 -0.79 0.27 0.36 -0.4 ... ..$ V42: num [1:799] 1.03 0.36 0.62 0.61 0.25 -1.06 0.35 0.37 0.55 -0.36 ... ..$ V43: num [1:799] 0.08 -0.26 -0.69 0.1 -0.09 -0.34 0.07 1.74 1.17 -0.16 ... ..$ V44: num [1:799] 0.57 0.11 0.47 0.47 0.16 -0.09 0.79 0.63 0.73 -0.57 ... ..$ V45: num [1:799] -0.26 -0.5 -0.48 -1.26 0.1 0.79 0.01 0.59 -0.73 -0.84 ... ..$ V46: num [1:799] -0.36 -0.66 NA -0.9 -0.04 0.6 -0.13 0.03 NA -0.52 ... ..$ V47: num [1:799] -0.55 -0.59 NA -0.63 0.03 0.66 -0.25 -0.33 NA 0.08 ... ..$ V48: num [1:799] -0.63 -0.05 -0.07 0.53 -0.14 -0.65 -1.04 -0.4 NA -2.01 ... ..$ V49: num [1:799] -0.66 -0.15 -0.58 -0.08 0.21 0.01 0.29 -0.99 -0.57 -1.25 ... ..$ V50: num [1:799] -0.24 -0.58 -0.05 -0.25 0.84 1.52 1.45 -1.06 -0.32 0.37 ... ..$ V51: num [1:799] -0.82 -0.58 0.16 1.95 0.19 0.48 0.67 -0.75 -0.87 0.82 ... ..$ V52: num [1:799] -0.84 0.18 0.64 2.39 -0.26 -0.34 -0.06 -0.61 -0.91 1.09 ... ..$ V53: num [1:799] -0.89 -0.67 -0.18 1.68 -0.1 -0.71 -0.5 -0.76 -1.65 -0.37 ... ..$ V54: num [1:799] 0.57 0.29 0.41 0.38 -0.03 -0.58 -0.49 0.71 -0.28 -0.22 ... ..$ V55: num [1:799] 0.64 0.2 0.02 -0.19 -0.09 -0.94 -0.83 1.49 0.15 -0.35 ... ..$ V56: num [1:799] 0.54 0.02 -0.31 -0.51 0 -0.6 -0.41 1.36 -0.05 -0.91 ... ..$ V57: num [1:799] 0.66 1.32 0.31 -0.02 -0.48 0.78 0.32 0.44 1.54 -0.4 ... ..$ V58: num [1:799] 0.28 0.27 0.18 -1.02 0.25 0.97 0.7 0.26 0.6 0.48 ... ..$ V59: num [1:799] -0.01 NA 0.18 -0.83 0.29 0.88 0.59 -0.13 NA 1.02 ... ..$ V60: num [1:799] -0.26 -0.41 -0.05 0.08 0.55 0.61 0.85 -0.36 -0.13 NA ... ..$ V61: num [1:799] 0.11 -0.05 -0.09 -1.66 -0.42 NA 0.09 NA 0.28 0.83 ... ..$ V62: num [1:799] NA 0.17 NA -0.37 NA -0.36 NA -0.11 0.77 0.58 ... ..$ V63: num [1:799] 0.71 0.14 -0.25 -1.83 -0.25 -0.71 -1.01 0.21 0.56 0.51 ... ..$ V64: num [1:799] 0.81 -0.11 -0.32 -0.25 -0.56 -0.33 -0.61 0.71 0.88 -0.21 ... ..$ V65: num [1:799] -1.16 -0.73 0.23 -0.2 -0.44 -0.83 0.1 -0.68 -1.02 -1.63 ... ..$ V66: num [1:799] -0.71 -0.05 -0.32 0.05 -0.69 -0.16 -0.34 -0.56 1.11 -1.22 ... ..$ V67: num [1:799] -0.71 -0.31 -0.42 0.03 -0.2 -0.69 -0.14 -0.59 0.34 -1.11 ... ..$ V68: num [1:799] -0.24 0.43 -0.28 0.29 -0.22 -0.24 -0.27 -0.27 0.18 -0.58 ... ..$ V69: num [1:799] -0.75 0.1 0.07 0.32 0.34 0.2 0.29 -0.36 0.16 0.11 ... ..$ V70: num [1:799] -0.11 0.12 -0.24 0.09 -0.02 0.51 0.69 -0.71 0.09 0.72 ... ..$ V71: num [1:799] -0.42 -0.4 -0.04 0.14 0.26 0.54 0.08 -0.29 0.16 1.18 ... ..$ V72: num [1:799] -0.01 -0.42 0.18 -0.05 0.49 0.45 0.12 0.21 -0.25 0.89 ... ..$ V73: num [1:799] 0.53 0.07 0.16 0.14 0.26 0.35 0.03 0.59 -0.41 0.87 ... ..$ V74: num [1:799] 0.58 0.19 0.04 -0.16 0.22 0.25 0.01 0.71 -0.09 0.42 ... ..$ V75: num [1:799] 1.49 -0.21 -0.2 0.12 0.07 -0.38 0.42 0.19 0.08 0.54 ... ..$ V76: num [1:799] 0.72 0.48 0.32 -0.09 0.01 0.24 -0.46 0.75 0 0.59 ... ..$ V77: num [1:799] 0.51 0.47 0.42 -0.29 -0.13 -0.09 -0.41 0.46 -0.32 -0.13 ... ..$ V78: num [1:799] 0.29 0.25 0.1 -0.39 0.05 -0.14 -0.12 0.54 -0.02 -0.65 ... $ n.changed: int 799 $ n.all : int 6179
total.data contains four components: 1) df.all: the whole microarray data set 1) df.ori: the differentially expressed gene data set 1) n.changed: the number of differentially expressed gene 1) n.all: the number of all genes in the whole data set
Spellman et. al (1998)
Further information about BNArray can be found at:
http://www.cls.zju.edu.cn/binfo/BNArray.
data(total.data) ## maybe str(total.data) ; plot(total.data) ...