spots 50 20 format labels ended ) Density measurements on 19 identifiable spots on each of 50 auto- ) radiographs, each spot corresponding to a particular (probably ) unknown) protein. ) ) The data in each row was derived from the blood of a rat subjected to ) a treatment expected to affect its thyroid hormones. ) There were 10 treatments in all, including a control (treatment 2). ) ) Col. 1: trt = treatment number (1-10) ) Col. 2-20: density measurements on spots 1-19. ) ) A 50 by 10 matrix of indicator dummy variables can be computed in ) MacAnova by ) Cmd> dummys <- 1*(spots[,1] == run(10)') ) A 50 by 9 matrix of contrast dummy variables (values 1, 0 or -1) ) comparing each group with group 10 can be computed from dummys by ) Cmd> design <- dummys[,-10] - dummys[,10] ) This contrast matrix is also available in this file as matrix 'design' ) You can read it by ) Cmd> design <- matread("cbspots.txt","design") ) )"%lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf %lf" (f2.0,4f4.0,f5.0,2f4.0,f3.0,f4.0,2f5.0,4f4.0,f3.0,3f4.0) 1 0 0 0 0 448 29 20 65 12 0 892 491 122 399 58 0 140 195 396 1 0 6 6 0 683 43 3 49 12 16 928 434 126 324 63 0 171 214 472 1 0 5 0 4 387 50 11 22 36 22 875 231 128 378 28 7 109 160 343 1 0 8 7 0 558 63 7 46 56 36 925 207 245 304 75 0 62 175 408 2 214 96 44 262 323 178 181 7 106 2482 515 179 55 164 37 0 41 137 125 2 259 198 48 202 596 160 182 11 194 2589 498 204 124 225 49 0 118 175 174 2 247 182 53 224 663 140 192 19 131 2678 610 112 111 176 50 0 61 208 172 2 274 148 50 217 704 208 134 8 70 2669 635 45 54 251 57 0 76 240 137 2 270 149 33 230 694 164 154 30 70 1866 558 201 65 155 46 0 76 227 218 2 242 188 36 220 724 202 138 29 72 2110 482 106 53 287 36 0 53 219 137 2 293 97 43 213 687 188 137 37 71 2138 446 127 47 311 46 0 58 239 151 2 189 208 30 203 735 203 162 25 167 2053 674 123 50 217 50 0 92 201 191 2 263 211 58 212 714 217 142 25 164 1916 535 118 108 249 73 0 136 254 199 2 219 200 51 215 683 169 133 12 171 2390 554 59 143 256 63 3 117 166 180 2 208 203 64 196 691 206 145 12 86 1930 511 93 58 152 56 0 97 186 163 3 180 69 22 188 659 130 138 21 2 632 1110 443 381 339 51 0 67 97 253 3 190 79 37 181 524 106 106 17 0 1336 1016 334 154 343 79 0 70 127 206 3 200 70 11 160 508 116 89 17 6 1246 1134 252 189 302 83 0 67 120 253 3 168 40 13 167 228 129 126 28 15 124 1092 243 305 341 84 0 57 147 279 3 162 58 21 160 538 122 106 71 1 212 1252 287 127 393 75 0 70 253 346 3 170 63 18 164 610 136 104 24 3 241 841 848 233 342 56 0 75 164 251 3 127 46 9 188 336 127 112 52 1 188 1230 427 309 372 84 0 73 238 347 4 84 105 43 109 64 256 211 19 233 129 498 110 94 312 73 0 43 220 201 4 102 83 37 30 67 229 189 24 168 19 816 174 138 452 130 0 34 99 222 4 132 78 37 184 110 360 176 15 285 88 703 157 81 379 92 0 51 222 147 5 203 92 23 333 894 196 112 19 3 569 1303 329 326 235 63 42 108 135 221 5 210 57 8 307 719 179 122 19 30 1489 1224 412 184 377 76 37 95 117 210 5 124 72 24 304 491 145 121 13 3 387 931 346 399 291 60 14 63 96 20 5 160 43 48 258 344 228 78 19 0 243 1191 280 143 359 35 15 38 139 230 5 83 76 17 273 332 131 106 30 2 322 1188 314 205 377 45 13 41 126 225 5 147 61 15 243 367 174 63 17 0 219 1203 267 181 342 48 17 45 171 221 5 114 65 19 251 454 140 108 13 1 115 1191 250 196 394 65 17 56 116 381 6 10 109 20 138 501 147 249 13 1 100 585 326 70 461 21 2 52 135 313 6 11 154 37 142 368 167 155 19 2 74 472 107 62 367 10 4 41 94 234 6 51 169 34 148 346 137 158 15 6 126 551 148 155 446 35 8 52 174 251 7 199 287 91 288 1287 265 99 20 0 269 1474 477 185 354 76 32 211 104 235 7 190 172 46 335 936 161 111 21 1 344 1170 587 187 338 83 52 111 164 209 8 126 308 73 146 46 363 86 11 494 335 260 60 29 55 12 3 25 269 163 8 133 151 106 160 11 255 73 10 537 95 376 70 22 23 12 1 30 261 187 8 131 224 76 131 75 265 72 12 423 767 396 70 24 44 54 4 32 221 166 8 110 247 71 176 75 286 52 11 426 571 335 87 27 58 29 0 50 331 187 8 93 258 89 190 151 278 102 14 668 899 389 58 37 46 29 1 45 251 173 9 177 163 59 230 139 378 191 23 116 1317 201 27 20 273 43 0 47 271 202 9 143 173 61 209 118 247 198 36 121 834 185 50 13 317 33 0 48 211 145 9 124 161 67 232 212 419 132 43 121 750 327 56 66 304 57 0 62 261 218 9 349 204 88 244 186 328 130 38 79 1147 256 54 36 387 75 0 52 202 161 10 215 468 124 134 101 477 202 9 688 1151 363 141 28 124 55 0 100 298 191 10 317 437 150 147 119 659 131 7 527 1745 393 134 37 107 48 0 70 219 155 10 311 285 158 122 110 365 180 13 639 966 306 127 51 109 45 0 94 167 113 10 283 368 106 150 144 682 159 4 703 1202 274 117 42 92 77 0 74 211 183 spots$labels 21 character columns ) Labels for matrix spots )"%s %s %s %s %s" # Group Sp01 Sp02 Sp03 Sp04 Sp05 Sp06 Sp07 Sp08 Sp09 Sp10 Sp11 Sp12 Sp13 Sp14 Sp15 Sp16 Sp17 Sp18 Sp19 %spots% design 50 9 format labels ) Dummy contrast variables for spot data ) Cols 1-9: dum1-dum9 = dummy variables for groups 1-9, Col. i coded 1 ) for group i, -1 for group 10, and 0 for other groups ) Sample sizes are 4, 11, 7, 3, 7, 3, 2, 5, 4, 4 ) Could be created by ) n <- rep(run(10), vector(4, 11, 7, 3, 7, 3, 2, 5, 4, 4)) ) design <- (1*(n == run(10)')) ) design <- design[,-10] - design[,10] )"%lf %lf %lf %lf %lf %lf %lf %lf %lf" (f2.0,8f3.0) 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 design$labels 59 quoted columns ) Labels for matrix design )"%s %s %s %s %s" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "@" "Dum1" "Dum2" "Dum3" "Dum4" "Dum5" "Dum6" "Dum7" "Dum8" "Dum9"