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Sample GSM91832 Query DataSets for GSM91832
Status Public on Jan 11, 2006
Title "083 Day8 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 "083 Day8 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "083 Day8 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/2001-10/21415.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 1561 1038 174 298 1387 740 958 707 465 550 784 409 0 0 1655 1027 3076 3053 15 2 2 1 2127 1193 1.874 .534 .522 .514 .443 2.835 80 542 .973 .96 110 1910 9320 34 45 44 55 -100 1048 301 747 .539 714 413 1.856 .527 -.892 -.924
2 261 366 147 274 114 92 238 326 183 287 91 52 0 0 126 156 165 133 30 37 6 16 206 143 1.239 .807 .571 .975 .933 3.698 80 384 1.19 .48 100 2090 9340 37 47 63 73 -50 370 277 93 .815 329 53 1.227 .577 -.295 -.793
3 1685 1416 140 263 1545 1153 1787 1380 158 274 1647 1117 0 0 808 716 126 97 97 91 93 86 2698 2764 1.34 .746 .678 .634 .747 1.955 80 328 .782 .9 100 2210 9330 36 46 75 85 0 1430 266 1165 .754 1394 1128 1.327 .685 -.408 -.546
4 3245 1032 143 266 3102 766 3226 903 163 288 3083 637 0 0 1334 486 125 132 100 96 100 93 3868 3720 4.05 .247 .207 .225 .235 1.564 80 426 .284 .57 110 2360 9330 35 46 89 100 0 1042 269 774 .249 912 643 4.009 .209 -2.003 -2.26
5 570 472 158 282 412 190 540 473 176 291 382 191 0 0 207 145 97 103 96 65 87 46 602 573 2.168 .461 .5 .443 .462 2.283 32 160 .375 .47 60 2510 9350 40 46 107 113 0 477 285 192 .466 478 193 2.147 .505 -1.102 -.986
6 4798 1212 151 260 4647 952 4810 1108 181 289 4659 848 0 0 1852 740 236 242 100 97 100 78 5599 5507 4.881 .205 .182 .188 .176 1.668 80 502 .19 .74 100 2680 9330 36 46 122 132 0 1224 263 962 .207 1119 857 4.832 .184 -2.273 -2.443
7 469 377 151 249 318 128 281 347 169 262 130 98 0 0 637 165 183 134 41 40 18 13 446 228 2.484 .403 .754 .781 .746 3.861 80 385 .933 .47 100 2870 9330 36 46 141 151 -50 381 252 129 .407 351 99 2.46 .761 -1.298 -.393
8 6559 3396 148 245 6411 3151 4624 1967 155 265 4476 1722 1 0 8567 4793 66 121 100 100 100 97 9562 6198 2.035 .491 .385 .401 .42 1.565 80 408 .502 .9 110 2990 9330 35 46 152 163 0 3430 247 3183 .496 1987 1739 2.014 .389 -1.01 -1.364
9 396 845 163 281 233 564 406 864 180 314 243 583 0 0 157 261 88 165 78 90 65 78 797 826 .413 2.421 2.399 2.251 2.164 1.873 32 215 2.494 .62 70 3130 9360 40 47 168 175 0 854 284 570 2.445 873 589 .409 2.423 1.29 1.277
10 393 666 163 279 230 387 410 640 182 295 247 361 0 0 120 208 95 124 84 90 65 65 617 608 .594 1.683 1.462 1.743 1.697 1.864 32 174 2.011 .69 60 3310 9360 41 47 187 193 0 673 282 391 1.7 646 365 .588 1.476 .765 .562
11 727 637 170 293 557 344 755 623 235 327 585 330 0 0 285 234 252 155 81 81 56 59 901 915 1.619 .618 .564 .579 .583 2.114 32 173 .681 .74 60 3470 9360 41 47 203 209 0 643 296 347 .624 629 333 1.603 .57 -.681 -.811
12 429 1324 186 410 243 914 383 1287 353 657 197 877 0 0 188 260 1116 1565 0 3 0 0 1157 1074 .266 3.761 4.452 4.054 3.675 2.034 32 217 1.696 .83 70 3640 9350 39 46 219 226 0 1337 414 923 3.799 1300 886 .263 4.497 1.926 2.169
13 279 583 190 423 89 160 243 526 347 671 53 103 0 0 142 230 1057 1731 0 0 0 0 249 156 .556 1.798 1.943 1.449 1.317 2.943 80 418 1.651 .94 100 3820 9330 36 46 236 246 -50 589 427 162 1.816 531 104 .551 1.963 .861 .973
14 2255 3163 177 394 2078 2769 1731 2672 222 470 1554 2278 0 0 1685 2292 217 355 85 85 80 79 4847 3832 .75 1.333 1.466 1.376 1.382 2.288 120 606 1.113 .88 130 3960 9320 33 46 248 261 -100 3195 398 2797 1.346 2699 2301 .743 1.481 .429 .566
15 463 1433 181 485 282 948 379 1047 240 571 198 562 0 0 286 1308 267 458 42 51 15 34 1230 760 .297 3.362 2.838 2.732 3.228 3.212 52 249 4.282 .68 80 4110 9330 37 45 266 274 -100 1447 490 958 3.396 1058 568 .294 2.867 1.764 1.52
16 1377 2238 171 394 1206 1844 994 1471 443 571 823 1077 0 0 1194 1930 2859 1316 13 44 0 28 3050 1900 .654 1.529 1.309 1.646 1.676 2.35 120 519 .577 .66 120 4280 9320 34 46 281 293 -100 2261 398 1863 1.544 1486 1088 .647 1.322 .627 .403
17 319 803 159 294 160 509 274 766 165 304 115 472 0 0 149 245 72 136 78 96 34 90 669 587 .314 3.181 4.104 3.697 3.75 2.811 32 155 3.747 .5 70 4410 9350 39 46 296 303 0 811 297 514 3.213 774 477 .311 4.146 1.684 2.052
18 268 507 149 287 119 220 250 430 180 309 101 143 0 0 114 273 328 185 3 41 0 21 339 244 .541 1.849 1.416 1.374 1 4.415 80 376 5.528 .26 100 4600 9330 36 46 314 324 -50 512 290 222 1.867 434 144 .536 1.43 .901 .516
19 1032 2440 145 299 887 2141 1023 2032 155 328 878 1733 0 0 509 1568 71 183 100 100 97 98 3028 2611 .414 2.414 1.974 2.343 2.152 1.821 80 401 3.074 .82 110 4730 9320 34 45 326 337 0 2465 302 2163 2.438 2053 1751 .41 1.994 1.286 .995
20 375 545 152 293 223 252 339 543 160 316 187 250 0 0 153 176 66 116 81 75 68 53 475 437 .885 1.13 1.337 1.017 .998 2.329 32 164 1.368 .31 60 4890 9320 37 43 345 351 0 551 296 255 1.141 548 253 .876 1.35 .191 .433

Total number of rows: 37632

Table truncated, full table size 8600 Kbytes.




Supplementary data files not provided
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