NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM91865 Query DataSets for GSM91865
Status Public on Jan 11, 2006
Title "003 Day0 in-vivo SP Inf, PBMC 3rd TC, 2nd amp"
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 Day0 in-vivo SP Inf, PBMC 3rd TC, 2nd amp"
Organism Homo sapiens
Characteristics "003 Day0 in-vivo SP Inf, PBMC 3rd TC, 2nd amp"
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/21426.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 1135 1310 197 503 938 807 897 1058 209 524 700 555 0 0 1043 977 94 201 76 78 70 62 1745 1255 1.162 .86 .793 .918 .89 2.833 156 856 .946 .84 140 1810 9120 29 43 33 47 0 1365 524 841 .896 1102 578 1.116 .826 -.158 -.276
2 624 1281 198 508 426 773 601 1246 209 526 403 738 0 0 272 475 94 178 90 88 76 86 1199 1141 .551 1.815 1.831 1.907 1.953 1.933 52 281 2.056 .77 90 1980 9100 29 38 52 61 0 1334 529 805 1.89 1298 769 .529 1.908 .919 .932
3 1718 2118 201 478 1517 1640 1341 1629 220 493 1140 1151 0 0 1283 1595 101 157 92 80 87 76 3157 2291 .925 1.081 1.01 .914 1.119 2.499 80 454 1.186 .94 110 2140 9100 28 39 67 78 0 2206 498 1708 1.126 1697 1199 .888 1.052 .171 .073
4 3266 1271 201 445 3065 826 3040 1138 215 463 2839 693 0 0 1888 719 93 129 97 86 96 77 3891 3532 3.711 .269 .244 .24 .273 1.914 80 435 .282 .88 110 2300 9100 28 39 83 94 0 1324 464 860 .281 1185 722 3.562 .254 -1.833 -1.976
5 575 905 201 437 374 468 410 684 216 457 209 247 0 0 516 617 97 145 66 68 50 45 842 456 .799 1.251 1.182 1.357 1.306 2.98 80 333 1.347 .81 100 2460 9120 31 41 100 110 -50 943 455 488 1.303 713 257 .767 1.231 .382 .3
6 7241 2727 204 465 7037 2262 5203 2136 218 476 4999 1671 0 0 5438 1824 132 139 100 97 100 96 9299 6670 3.111 .321 .334 .308 .307 1.759 80 387 .307 .92 100 2600 9100 29 39 114 124 0 2841 484 2356 .335 2225 1741 2.987 .348 -1.578 -1.522
7 299 582 210 452 89 130 230 534 219 463 20 82 0 0 197 245 139 123 33 41 17 23 219 102 .685 1.461 4.1 1.167 1.308 2.982 80 339 1.552 .53 100 2780 9120 31 41 132 142 -50 606 471 135 1.522 556 85 .657 4.271 .606 2.095
8 2777 1548 208 443 2569 1105 2110 1068 211 449 1902 625 0 0 2500 1210 86 129 97 88 96 70 3674 2527 2.325 .43 .329 .394 .421 2.031 120 428 .443 .93 120 2920 9100 28 40 145 157 0 1613 461 1151 .448 1113 651 2.232 .342 -1.158 -1.547
9 573 1975 193 460 380 1515 463 1451 207 481 270 991 0 0 379 1354 134 195 65 86 50 75 1895 1261 .251 3.987 3.67 4.066 3.919 2.159 80 393 3.888 .85 110 3060 9110 29 40 159 170 0 2057 479 1578 4.153 1511 1032 .241 3.823 2.054 1.935
10 656 1462 187 474 469 988 535 1121 205 488 348 647 0 0 372 899 102 145 86 84 73 69 1457 995 .475 2.107 1.859 1.82 2.042 1.981 52 275 2.558 .82 80 3230 9110 31 39 178 186 0 1523 494 1029 2.194 1168 674 .456 1.937 1.134 .954
11 1305 1665 253 561 1052 1104 1506 1598 326 647 1253 1037 0 0 608 790 278 296 81 78 68 71 2156 2290 .953 1.049 .828 1.037 1.099 1.854 32 225 1.186 .86 70 3380 9120 32 39 193 200 0 1734 584 1150 1.093 1665 1080 .915 .862 .128 -.214
12 633 1957 247 704 386 1253 615 1905 282 769 368 1201 0 0 208 682 152 390 84 90 59 75 1639 1569 .308 3.246 3.264 3.015 3.079 1.856 32 206 4.153 .71 70 3540 9090 29 36 209 216 0 2039 733 1305 3.381 1984 1251 .296 3.4 1.758 1.765
13 1403 1952 255 453 1148 1499 1221 1977 304 494 966 1524 0 0 601 388 152 181 100 100 100 100 2647 2490 .766 1.306 1.578 1.404 1.521 1.515 12 84 1.382 .79 50 3720 9100 31 36 228 233 0 2033 472 1561 1.36 2059 1588 .735 1.643 .444 .717
14 1935 2269 218 463 1717 1806 1273 1726 238 480 1055 1263 0 0 1634 1925 112 160 95 95 91 87 3523 2318 .951 1.052 1.197 1.013 1.096 2.159 120 587 1.136 .94 120 3860 9100 28 40 239 251 0 2364 482 1881 1.096 1798 1316 .913 1.247 .132 .319
15 927 1869 257 520 670 1349 871 2025 287 563 614 1505 0 0 417 814 147 220 87 87 84 84 2019 2119 .497 2.013 2.451 1.954 1.905 1.737 32 156 2.151 .85 60 4030 9120 33 39 259 265 0 1947 542 1405 2.097 2109 1568 .477 2.553 1.069 1.352
16 2885 4408 229 480 2656 3928 2178 3662 257 509 1949 3182 0 0 2039 3381 180 243 98 94 90 86 6584 5131 .676 1.479 1.633 1.222 1.456 2.18 52 333 1.6 .95 90 4180 9090 28 37 272 281 0 4592 500 4092 1.541 3815 3315 .649 1.701 .623 .766
17 353 677 223 446 130 231 283 575 269 469 60 129 0 0 239 403 190 156 25 43 13 22 361 189 .563 1.777 2.15 1.731 1.854 2.53 80 433 1.602 .56 100 4340 9120 31 41 288 298 -50 705 465 241 1.851 599 134 .54 2.24 .888 1.163
18 422 692 211 450 211 242 333 567 221 466 122 117 0 0 312 372 79 131 58 50 40 32 453 239 .872 1.147 .959 1.443 1.245 3.014 80 321 1.291 .75 100 4500 9120 31 41 304 314 -50 721 469 252 1.195 591 122 .837 .999 .257 -.001
19 887 3520 212 472 675 3048 792 2491 224 523 580 2019 0 0 417 2075 105 291 97 97 91 96 3723 2599 .221 4.516 3.481 4.456 4.465 1.521 80 441 4.922 .91 110 4620 9090 27 38 315 326 0 3667 492 3175 4.704 2595 2103 .213 3.626 2.234 1.858
20 747 1325 238 539 509 786 753 1146 251 541 515 607 0 0 197 548 88 160 100 91 100 91 1295 1122 .648 1.544 1.179 1.471 1.441 1.961 12 72 2.295 .71 50 4800 9080 29 34 336 341 0 1380 561 819 1.609 1194 632 .622 1.228 .686 .296

Total number of rows: 37632

Table truncated, full table size 8617 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap