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Sample GSM91868 Query DataSets for GSM91868
Status Public on Jan 11, 2006
Title "003 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 "003 Day4 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "003 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/2001-10/21428.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 3223 1954 288 569 2935 1385 2737 1616 338 608 2449 1047 0 0 2024 1086 258 211 96 88 90 73 4320 3496 2.119 .472 .428 .441 .482 1.865 52 341 .489 .94 90 1760 9430 78 87 32 41 0 1826 532 1294 .441 1510 979 2.267 .4 -1.181 -1.324
2 1279 2662 321 630 958 2032 1248 2581 336 670 927 1951 0 0 565 1234 129 224 93 100 93 96 2990 2878 .471 2.121 2.105 2.168 2.236 1.822 32 148 2.244 .9 60 1930 9430 80 86 51 57 0 2488 589 1899 1.982 2412 1823 .504 1.967 .987 .976
3 3092 4139 283 575 2809 3564 2236 3260 312 622 1953 2685 0 0 1873 2384 181 265 100 100 100 94 6373 4638 .788 1.269 1.375 1.262 1.299 1.303 52 352 1.284 .96 90 2080 9450 80 89 64 73 0 3868 537 3331 1.186 3047 2509 .843 1.285 .246 .362
4 6044 2439 267 542 5777 1897 5402 2117 281 563 5135 1575 0 0 2927 1100 119 171 100 100 100 94 7674 6710 3.045 .328 .307 .305 .332 1.458 52 357 .331 .96 90 2240 9440 79 88 80 89 0 2279 507 1773 .307 1979 1472 3.259 .287 -1.704 -1.803
5 2917 2688 383 658 2534 2030 3064 2693 399 701 2681 2035 0 0 1137 692 161 213 100 100 100 100 4564 4716 1.248 .801 .759 .843 .734 1.291 12 90 .739 .92 50 2380 9440 81 86 96 101 0 2512 615 1897 .749 2517 1902 1.336 .709 -.418 -.495
6 11000 4280 265 569 10735 3711 8559 3296 295 594 8294 2727 0 0 7105 2537 122 170 100 100 100 98 14446 11021 2.893 .346 .329 .334 .337 1.352 80 447 .346 .97 100 2550 9440 79 89 111 121 0 4000 532 3468 .323 3080 2549 3.095 .307 -1.63 -1.702
7 426 823 265 576 161 247 337 633 284 598 72 57 0 0 277 527 107 170 41 37 25 22 408 129 .652 1.534 .792 1.667 1.585 3.28 80 336 2.194 .73 100 2720 9460 81 91 128 138 -50 769 538 231 1.434 592 53 .697 .74 .52 -.435
8 4944 2568 281 616 4663 1952 4456 2120 294 725 4175 1504 0 0 3572 1591 116 451 92 82 88 74 6615 5679 2.389 .419 .36 .432 .424 2.195 120 517 .413 .9 120 2860 9430 77 89 141 153 0 2400 576 1824 .391 1981 1406 2.556 .337 -1.354 -1.571
9 921 3347 277 638 644 2709 1018 3405 304 678 741 2767 0 0 473 1735 129 258 81 87 78 84 3353 3508 .238 4.207 3.734 3.426 3.675 2.166 32 226 4.209 .89 70 3030 9450 81 88 160 167 0 3128 596 2532 3.931 3182 2586 .254 3.49 1.975 1.803
10 1720 3672 368 795 1352 2877 1814 3734 409 810 1446 2939 0 0 640 1168 181 303 91 100 83 100 4229 4385 .47 2.128 2.033 2.479 2.089 1.713 12 72 2.14 .93 50 3170 9420 79 84 175 180 0 3432 743 2689 1.989 3490 2747 .503 1.9 .992 .926
11 1304 1883 278 613 1026 1270 1151 1797 316 645 873 1184 0 0 860 1127 169 223 82 80 69 69 2296 2057 .808 1.238 1.356 1.264 1.237 3.244 52 348 1.314 .92 90 3300 9440 79 88 186 195 0 1760 573 1187 1.157 1679 1107 .864 1.268 .21 .342
12 788 1572 273 588 515 984 572 1181 293 604 299 593 0 0 509 982 130 179 78 82 55 68 1499 892 .523 1.911 1.983 2.008 2.088 2.09 80 424 2.033 .89 100 3480 9430 78 88 204 214 0 1469 550 920 1.786 1104 554 .56 1.854 .836 .89
13 634 1162 258 559 376 603 468 838 267 597 210 279 0 0 465 811 93 167 70 62 56 45 979 489 .624 1.604 1.329 1.228 1.505 3.849 80 387 1.828 .86 100 3660 9450 80 90 222 232 -50 1086 522 564 1.499 783 261 .667 1.242 .584 .312
14 3645 5529 259 556 3386 4973 2548 3779 281 595 2289 3223 0 0 2846 4227 123 208 100 100 100 96 8359 5512 .681 1.469 1.408 1.431 1.502 1.557 80 468 1.496 .97 110 3800 9440 78 89 235 246 0 5167 520 4648 1.373 3532 3012 .729 1.316 .457 .396
15 1295 2742 283 593 1012 2149 1399 2722 316 645 1116 2129 0 0 689 1588 152 263 84 84 78 81 3161 3245 .471 2.124 1.908 2.199 2.079 1.382 32 200 2.285 .94 70 3980 9450 81 88 255 262 0 2563 554 2008 1.985 2544 1990 .504 1.783 .989 .834
16 3101 5390 267 590 2834 4800 2126 3661 282 605 1859 3071 0 0 2636 4622 101 168 98 98 96 97 7634 4930 .59 1.694 1.652 1.661 1.735 1.503 80 398 1.751 .96 100 4120 9430 78 88 268 278 0 5037 551 4486 1.583 3421 2870 .632 1.544 .663 .627
17 610 1147 264 650 346 497 492 839 309 669 228 189 0 0 392 720 323 242 35 43 21 33 843 417 .696 1.436 .829 1.276 1.449 2.581 80 393 1.893 .82 100 4290 9450 80 90 285 295 -50 1072 607 464 1.342 784 177 .745 .775 .425 -.368
18 631 1295 263 690 368 605 440 979 315 723 177 289 0 0 480 843 343 262 30 53 20 31 973 466 .608 1.644 1.633 1.787 1.76 2.646 80 352 1.922 .82 100 4450 9450 80 90 301 311 -50 1210 645 565 1.536 915 270 .651 1.526 .62 .61
19 1421 5333 282 719 1139 4614 1279 5048 306 740 997 4329 0 0 739 2989 153 213 95 97 88 97 5753 5326 .247 4.051 4.342 4.031 4.227 1.543 80 438 4.212 .93 110 4590 9430 77 88 314 325 0 4984 672 4312 3.786 4718 4046 .264 4.058 1.921 2.021
20 1033 2159 397 889 636 1270 1143 1909 391 914 746 1020 0 0 381 539 148 205 75 100 75 100 1906 1766 .501 1.997 1.367 2.533 2.473 2.372 12 64 2.139 .76 50 4750 9410 78 83 333 338 0 2018 831 1187 1.866 1784 953 .536 1.278 .9 .354

Total number of rows: 37632

Table truncated, full table size 8664 Kbytes.




Supplementary data files not provided
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