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Sample GSM91728 Query DataSets for GSM91728
Status Public on Jan 11, 2006
Title "409 Day11 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 Day11 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "409 Day11 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/2001-10/21438.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 1289 805 148 343 1141 462 906 677 170 378 758 334 0 0 1036 457 130 157 93 70 83 53 1603 1092 2.47 .405 .441 .442 .429 2.29 80 480 .402 .86 110 1860 9490 53 64 47 58 0 970 413 557 .488 816 402 2.05 .531 -1.036 -.914
2 290 641 153 366 137 275 225 564 174 400 72 198 0 0 177 333 144 165 35 53 20 31 412 270 .498 2.007 2.75 2.001 2.098 3.515 80 376 2.741 .61 100 2050 9510 56 66 67 77 -50 772 441 331 2.418 680 239 .413 3.313 1.274 1.728
3 1366 1495 152 359 1214 1136 1209 1309 155 381 1057 950 0 0 755 823 60 142 96 92 95 87 2350 2007 1.069 .936 .899 .883 .923 1.611 80 352 .942 .91 100 2190 9490 54 64 81 91 0 1801 433 1369 1.127 1577 1145 .887 1.083 .173 .115
4 2704 1112 159 402 2545 710 2646 1074 165 431 2487 672 0 0 1413 502 63 177 97 85 97 73 3255 3159 3.585 .279 .27 .275 .288 1.848 80 403 .278 .87 100 2350 9490 54 64 97 107 0 1340 484 855 .336 1294 810 2.975 .326 -1.573 -1.619
5 386 504 161 411 225 93 300 433 167 449 139 22 0 0 315 269 68 181 57 25 50 17 318 161 2.419 .413 .158 .854 .857 3.359 80 342 1.061 .6 100 2530 9510 56 66 115 125 -50 607 495 112 .498 522 27 2.008 .191 -1.006 -2.391
6 6226 2472 139 337 6087 2135 5249 2078 150 356 5110 1741 0 0 4036 1581 62 125 100 96 100 95 8222 6851 2.851 .351 .341 .32 .34 1.653 80 443 .354 .95 110 2650 9490 53 64 126 137 0 2978 406 2572 .423 2504 2098 2.366 .41 -1.243 -1.285
7 215 415 149 336 66 79 174 392 194 393 25 56 0 0 145 179 308 309 11 12 0 1 145 81 .835 1.197 2.24 1.726 1.716 2.982 80 380 2.182 .38 100 2840 9500 55 65 146 156 -50 500 405 95 1.442 472 67 .693 2.699 .528 1.432
8 2603 1115 167 385 2436 730 2066 953 285 488 1899 568 0 0 1747 717 457 444 86 51 76 34 3166 2467 3.337 .3 .299 .286 .318 2.449 52 307 .332 .76 90 2960 9500 55 64 158 167 0 1343 464 880 .361 1148 684 2.77 .36 -1.47 -1.472
9 467 992 149 381 318 611 500 985 175 405 351 604 0 0 215 444 89 162 81 87 71 75 929 955 .52 1.921 1.721 2.313 1.97 1.94 32 225 2.138 .83 70 3140 9510 57 64 177 184 0 1195 459 736 2.315 1187 728 .432 2.073 1.211 1.052
10 676 1217 188 446 488 771 680 1219 201 480 492 773 0 0 110 219 80 168 100 100 100 100 1259 1265 .633 1.58 1.571 1.558 1.554 1.36 12 80 1.725 .85 50 3280 9480 55 60 192 197 0 1466 537 929 1.904 1469 931 .525 1.893 .929 .921
11 352 527 159 379 193 148 211 471 173 395 52 92 0 0 309 271 94 144 40 40 31 20 341 144 1.304 .767 1.769 1.357 1.209 4.283 80 440 1.046 .71 100 3470 9500 55 65 209 219 -50 635 457 178 .924 567 111 1.082 2.132 -.114 1.092
12 555 1134 180 395 375 739 520 1149 190 416 340 754 0 0 131 257 92 149 100 100 91 91 1114 1094 .507 1.971 2.218 1.92 2.281 1.676 12 76 2.108 .79 50 3600 9480 55 60 224 229 0 1366 476 890 2.374 1384 908 .421 2.672 1.248 1.418
13 264 502 137 350 127 152 211 432 147 366 74 82 0 0 161 261 65 128 52 38 40 22 279 156 .836 1.197 1.108 1.174 1.466 2.9 80 390 2.255 .62 100 3780 9500 55 65 240 250 -50 605 422 183 1.442 520 99 .693 1.335 .528 .417
14 1370 1542 141 366 1229 1176 1059 1191 160 395 918 825 0 0 1132 1150 144 210 87 81 80 70 2405 1743 1.045 .957 .899 .963 .957 2.348 80 416 1.002 .95 110 3900 9470 51 62 251 262 0 1858 441 1417 1.153 1435 994 .867 1.083 .205 .115
15 289 607 139 362 150 245 206 468 156 379 67 106 0 0 224 398 129 172 33 43 21 27 395 173 .612 1.633 1.582 1.851 1.733 2.667 80 381 1.997 .77 100 4100 9500 55 65 272 282 -50 731 436 295 1.968 564 128 .508 1.906 .977 .931
16 1011 2113 139 352 872 1761 749 1493 143 365 610 1141 0 0 820 1654 55 127 94 95 91 88 2633 1751 .495 2.019 1.87 2.034 1.994 1.654 120 518 2.093 .94 120 4230 9480 52 64 284 296 0 2546 424 2122 2.433 1799 1375 .411 2.254 1.283 1.172
17 208 462 143 354 65 108 170 412 148 368 27 58 0 0 137 251 57 123 36 35 23 25 173 85 .602 1.662 2.148 1.855 2.09 3.975 80 423 3.062 .53 100 4410 9500 55 65 303 313 -50 557 427 130 2.002 496 70 .5 2.588 1.001 1.372
18 618 693 141 330 477 363 615 781 157 348 474 451 0 0 180 229 64 138 100 83 100 75 840 925 1.314 .761 .951 .731 .845 1.68 12 80 1.12 .74 50 4550 9470 54 59 319 324 0 835 398 437 .917 941 543 1.091 1.146 -.125 .197
19 628 1029 132 313 496 716 638 1026 147 331 506 713 0 0 254 380 73 135 92 94 92 86 1212 1219 .693 1.444 1.409 1.497 1.545 1.77 52 296 1.612 .85 80 4690 9470 53 61 332 340 0 1240 377 863 1.739 1236 859 .575 1.698 .798 .764
20 208 391 136 322 72 69 170 359 145 340 34 37 0 0 140 154 67 138 40 28 22 8 141 71 1.043 .958 1.088 1.162 .948 4.346 80 410 1.83 .41 100 4890 9490 54 64 351 361 -50 471 388 83 1.155 433 45 .866 1.311 .207 .391

Total number of rows: 37632

Table truncated, full table size 8474 Kbytes.




Supplementary data files not provided
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