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Sample GSM91737 Query DataSets for GSM91737
Status Public on Jan 11, 2006
Title "57-394 Day6 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 "57-394 Day6 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "57-394 Day6 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/2001-10/21515.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 1275 1148 146 428 1129 720 1008 932 174 466 862 504 0 0 843 686 138 256 88 65 80 50 1849 1366 1.568 .638 .585 .628 .697 2.209 52 255 .773 .8 80 1720 9400 62 70 40 48 0 1531 571 960 .85 1243 672 1.176 .78 -.234 -.359
2 271 634 147 413 124 221 235 609 165 462 88 196 0 0 156 282 117 284 40 38 21 13 345 284 .561 1.782 2.227 2.108 1.908 3.515 80 369 3.07 .63 100 1890 9420 63 73 56 66 -50 845 551 295 2.376 812 261 .421 2.97 1.249 1.57
3 1503 2092 136 402 1367 1690 1156 1622 167 471 1020 1220 0 0 996 1400 140 325 94 88 90 75 3057 2240 .809 1.236 1.196 1.142 1.125 1.998 52 270 1.374 .9 90 2030 9390 60 69 70 79 0 2789 536 2253 1.648 2163 1627 .607 1.595 .721 .673
4 2419 1486 132 414 2287 1072 1848 1212 146 433 1716 798 0 0 1715 869 83 206 98 86 98 73 3359 2514 2.133 .469 .465 .451 .478 1.851 80 394 .446 .87 100 2170 9390 60 70 84 94 0 1981 552 1429 .625 1616 1064 1.6 .62 -.678 -.69
5 444 747 142 404 302 343 218 549 167 418 76 145 0 0 479 600 133 187 45 45 31 31 645 221 .88 1.136 1.908 1.834 1.548 3.359 80 379 1.416 .73 100 2360 9420 63 73 103 113 -50 996 539 457 1.514 732 193 .66 2.544 .599 1.347
6 5956 2844 128 376 5828 2468 4656 2364 135 395 4528 1988 0 0 4503 1900 57 177 100 93 100 88 8296 6516 2.361 .423 .439 .434 .414 1.518 80 345 .406 .95 100 2490 9380 59 69 116 126 0 3792 501 3291 .565 3152 2651 1.771 .585 -.825 -.773
7 174 435 134 381 40 54 134 386 144 413 0 5 0 0 138 224 69 201 23 20 12 8 94 5 .741 1.35 null 2.349 2.211 5.611 80 355 7.874 .22 100 2670 9420 63 73 134 144 -50 580 508 72 1.8 515 7 .556 null .848 null
8 1850 1389 139 390 1711 999 1073 931 152 425 934 541 0 0 1871 1059 102 180 87 73 81 63 2710 1475 1.713 .584 .579 .657 .57 1.912 80 424 .531 .88 110 2800 9380 58 69 146 157 0 1852 520 1332 .778 1241 721 1.285 .772 -.361 -.373
9 522 1212 143 447 379 765 454 1152 160 501 311 705 0 0 284 531 77 220 87 84 84 71 1144 1016 .495 2.018 2.267 2.248 1.707 2.537 32 184 2.873 .67 70 2960 9380 60 67 164 171 0 1616 596 1020 2.691 1536 940 .372 3.023 1.428 1.596
10 2463 9180 174 561 2289 8619 951 2132 242 609 777 1571 0 0 4346 16969 219 333 91 100 66 91 10908 2348 .266 3.765 2.022 2.297 2.074 1.759 12 80 3.99 .97 50 3100 9390 62 67 179 184 -100 12240 748 11492 5.021 2843 2095 .199 2.696 2.328 1.431
11 593 1024 146 405 447 619 676 999 158 425 530 594 0 0 346 503 68 190 75 81 75 68 1066 1124 .722 1.385 1.121 1.605 1.521 2.255 32 134 1.728 .74 60 3270 9390 62 68 196 202 0 1365 540 825 1.846 1332 792 .542 1.494 .885 .58
12 594 994 153 407 441 587 559 886 160 439 406 479 0 0 318 470 65 194 84 81 81 62 1028 885 .751 1.331 1.18 1.603 1.5 2.153 32 122 1.725 .7 60 3440 9380 61 67 213 219 0 1325 543 783 1.775 1181 639 .563 1.573 .828 .654
13 361 825 140 403 221 422 232 700 148 427 92 297 0 0 309 540 62 182 57 62 42 40 643 389 .524 1.91 3.228 2.19 1.861 2.462 80 372 2.249 .77 100 3610 9410 62 72 228 238 -50 1100 537 563 2.546 933 396 .393 4.304 1.348 2.106
14 1319 2674 138 397 1181 2277 604 1387 147 425 466 990 0 0 1562 3014 63 185 83 84 77 70 3458 1456 .519 1.928 2.124 1.986 2.054 2.044 120 457 1.963 .97 120 3760 9390 59 71 242 254 -100 3565 529 3036 2.571 1849 1320 .389 2.833 1.362 1.502
15 317 660 149 430 168 230 197 485 188 561 48 55 0 0 297 465 166 611 32 20 18 7 398 103 .73 1.369 1.146 1.921 1.502 3.443 80 377 3.89 .68 100 3920 9410 62 72 259 269 -50 880 573 307 1.825 647 73 .548 1.528 .868 .611
16 1962 7148 144 446 1818 6702 1004 3764 193 631 860 3318 0 0 1741 6342 189 803 90 86 80 78 8520 4178 .271 3.686 3.858 3.467 3.627 1.554 52 296 3.739 .98 90 4080 9380 59 68 275 284 -100 9531 595 8936 4.915 5019 4424 .203 5.144 2.297 2.363
17 293 610 143 404 150 206 202 469 165 444 59 65 0 0 221 387 125 432 37 22 21 6 356 124 .728 1.373 1.102 2.034 1.589 3.662 80 414 2.445 .58 100 4230 9410 62 72 290 300 -50 813 539 275 1.831 625 87 .546 1.469 .873 .555
18 290 602 142 395 148 207 170 559 148 412 28 164 0 0 273 291 62 178 37 47 28 23 355 192 .715 1.399 5.857 2.043 1.941 4.592 80 336 1.763 .56 100 4390 9410 62 72 306 316 -50 803 527 276 1.865 745 219 .536 7.81 .899 2.965
19 736 1685 154 397 582 1288 746 1698 158 424 592 1301 0 0 363 797 63 186 96 91 95 86 1870 1893 .452 2.213 2.198 2.206 2.246 1.635 80 381 2.404 .9 100 4520 9390 60 70 319 329 0 2247 529 1717 2.951 2264 1735 .339 2.93 1.561 1.551
20 857 1121 158 391 699 730 860 1165 160 436 702 774 0 0 191 326 56 190 100 100 100 83 1429 1476 .958 1.044 1.103 .972 .977 1.578 12 64 1.43 .69 50 4680 9370 60 65 337 342 0 1495 521 973 1.392 1553 1032 .718 1.47 .478 .556

Total number of rows: 37632

Table truncated, full table size 8420 Kbytes.




Supplementary data files not provided
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