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Sample GSM91721 Query DataSets for GSM91721
Status Public on Jan 11, 2006
Title "409 Day4 in-vivo SP Inf, PBMC 3rd TC"
Sample type RNA
 
Channel 1
Source name "CRG, 1 round of amplification, Addie and Kate from 7/19/01"
Organism Homo sapiens
Characteristics "CRG, 1 round of amplification, Addie and Kate from 7/19/01"
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name "409 Day4 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "409 Day4 in-vivo SP Inf, PBMC 3rd TC"
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/21435.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jan 10, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3093
Series (1)
GSE4013 Host response to smallpox

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 1687 972 174 393 1513 579 1311 785 211 409 1137 392 0 0 1303 578 193 145 87 77 81 57 2092 1529 2.613 .383 .345 .354 .39 2.006 80 379 .388 .89 100 1870 9330 34 44 49 59 0 962 389 573 .379 777 388 2.639 .341 -1.4 -1.551
2 319 558 181 403 138 155 269 506 209 426 88 103 0 0 198 265 161 153 32 43 18 27 293 191 .89 1.123 1.17 1.575 1.533 2.752 80 387 1.562 .64 100 2070 9350 36 46 69 79 -50 552 399 153 1.112 501 102 .899 1.159 .153 .213
3 1756 2014 188 402 1568 1612 1523 1685 270 461 1335 1283 0 0 1020 1134 348 264 90 96 76 76 3180 2618 .973 1.028 .961 1.034 1.011 1.561 52 276 1.054 .94 90 2190 9320 33 42 81 90 0 1994 398 1596 1.018 1668 1270 .982 .952 .026 -.072
4 2917 958 192 393 2725 565 2220 790 273 431 2028 397 0 0 2186 631 352 227 86 65 82 46 3290 2425 4.823 .207 .196 .236 .237 2.935 52 358 .228 .9 90 2360 9350 36 45 98 107 0 949 389 559 .205 782 393 4.871 .194 -2.284 -2.367
5 453 558 177 365 276 193 283 476 188 380 106 111 0 0 418 305 99 122 53 46 38 32 469 217 1.43 .699 1.047 1.038 .909 2.91 80 360 .727 .74 100 2540 9350 36 46 116 126 -50 552 361 191 .692 471 110 1.444 1.037 -.53 .052
6 8487 2664 162 318 8325 2346 7818 2400 186 343 7656 2082 0 0 5505 1698 143 122 100 93 100 92 10671 9738 3.549 .282 .272 .265 .278 1.572 80 446 .286 .97 110 2670 9350 35 46 128 139 0 2638 315 2323 .279 2376 2061 3.584 .269 -1.842 -1.893
7 226 322 153 285 73 37 183 287 170 297 30 2 0 0 130 183 91 104 32 22 15 13 110 32 1.973 .507 .067 .9 1.199 5.46 80 351 1.306 .44 100 2860 9350 36 46 148 158 -50 319 282 37 .502 284 2 1.993 .066 -.995 -3.921
8 2356 1430 171 269 2185 1161 1437 1013 236 307 1266 744 0 0 2035 1146 323 192 87 83 72 68 3346 2010 1.882 .531 .588 .548 .528 1.944 80 442 .543 .96 110 2960 9340 34 45 157 168 0 1416 266 1150 .526 1003 737 1.901 .582 -.927 -.781
9 467 865 184 271 283 594 463 922 197 295 279 651 0 0 252 461 81 140 71 81 62 68 877 930 .476 2.099 2.333 2.337 1.987 1.716 32 176 2.007 .86 60 3150 9360 39 45 179 185 0 856 268 588 2.078 913 645 .481 2.31 1.055 1.208
10 325 499 181 245 144 254 231 329 191 256 50 84 0 0 248 398 83 89 43 50 31 36 398 134 .567 1.764 1.68 1.479 1.516 2.911 80 422 1.625 .78 100 3330 9350 36 46 195 205 -50 494 243 251 1.746 326 83 .573 1.663 .804 .734
11 746 726 194 251 552 475 803 807 202 257 609 556 0 0 335 342 90 89 84 78 84 71 1027 1165 1.162 .861 .913 .746 .878 2.488 32 152 .929 .88 60 3470 9350 38 44 211 217 0 719 249 470 .852 799 550 1.174 .904 -.231 -.146
12 506 665 167 228 339 437 415 677 180 244 248 449 0 0 278 317 67 94 78 84 68 75 776 697 .776 1.289 1.81 1.204 1.216 2.43 32 188 1.462 .79 70 3610 9320 34 41 224 231 0 658 226 433 1.276 670 445 .784 1.793 .352 .842
13 274 423 165 235 109 188 225 332 175 251 60 97 0 0 183 253 67 95 46 50 30 35 297 157 .58 1.725 1.617 1.187 1.22 3.787 80 393 1.614 .68 100 3800 9360 37 47 242 252 -50 419 233 186 1.708 329 96 .586 1.601 .772 .679
14 1417 1979 168 260 1249 1719 935 1168 177 277 767 908 0 0 1338 1823 70 103 91 87 77 80 2968 1675 .727 1.376 1.184 1.363 1.42 1.715 80 407 1.381 .96 100 3930 9340 35 45 255 265 0 1959 257 1702 1.363 1156 899 .734 1.172 .446 .229
15 714 1123 218 368 496 755 726 1265 232 380 508 897 0 0 257 372 97 122 100 100 75 83 1251 1405 .657 1.522 1.766 1.498 1.489 1.399 12 90 1.516 .89 50 4100 9340 37 42 274 279 0 1112 364 748 1.507 1252 888 .664 1.748 .592 .806
16 1382 2950 185 318 1197 2632 721 1698 226 405 536 1380 0 0 1360 2931 355 762 72 65 41 47 3829 1916 .455 2.199 2.575 2.109 2.291 1.859 80 529 1.011 .94 110 4240 9330 33 44 285 296 0 2921 315 2606 2.177 1681 1366 .459 2.549 1.122 1.35
17 492 790 200 373 292 417 542 855 215 389 342 482 0 0 136 202 85 133 91 83 83 83 709 824 .7 1.428 1.409 1.364 1.63 2.545 12 90 1.395 .7 50 4400 9340 37 42 304 309 0 782 369 413 1.414 847 477 .707 1.395 .5 .481
18 298 440 178 338 120 102 245 378 183 356 67 40 0 0 179 214 71 123 45 35 35 21 222 107 1.176 .85 .597 1.077 .988 4.068 80 389 1.758 .5 100 4580 9360 37 47 320 330 -50 436 335 101 .842 374 40 1.188 .591 -.249 -.759
19 691 1458 173 331 518 1127 628 1227 179 353 455 896 0 0 376 785 71 139 87 95 83 91 1645 1351 .46 2.176 1.969 2.369 2.197 1.852 80 424 2.261 .9 110 4710 9340 34 45 332 343 0 1444 328 1116 2.154 1215 887 .464 1.95 1.107 .963
20 262 429 173 341 89 88 214 362 198 368 41 21 0 0 171 239 139 166 27 28 15 16 177 62 1.011 .989 .512 1.668 1.514 3.289 80 415 2.094 .54 100 4900 9360 37 47 352 362 -50 425 338 87 .979 358 21 1.021 .507 -.031 -.98

Total number of rows: 37632

Table truncated, full table size 8472 Kbytes.




Supplementary data files not provided
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