NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM91795 Query DataSets for GSM91795
Status Public on Jan 11, 2006
Title "282 Day -4 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 "282 Day -4 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "282 Day -4 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/2001-10/21479.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 1037 571 104 220 933 351 826 506 117 238 722 286 0 0 721 258 61 114 97 85 95 60 1284 1008 2.658 .376 .396 .408 .388 2.485 80 386 .327 .74 100 2040 9410 44 54 44 54 0 1057 407 650 .697 937 530 1.435 .734 -.521 -.447
2 226 340 107 208 119 132 181 297 130 232 74 89 0 0 153 177 131 133 35 40 20 23 251 163 .902 1.109 1.203 1.277 1.181 2.979 80 394 1.713 .55 100 2240 9410 44 54 64 74 -50 630 385 244 2.054 550 165 .487 2.227 1.039 1.155
3 1359 1024 111 221 1248 803 1304 1007 164 263 1193 786 0 0 627 473 226 214 96 94 92 71 2051 1979 1.554 .643 .659 .676 .691 1.651 52 275 .691 .87 90 2350 9390 42 51 75 84 0 1896 409 1487 1.192 1865 1456 .839 1.22 .253 .287
4 2381 726 111 214 2270 512 2485 697 144 249 2374 483 0 0 973 302 184 187 100 88 100 62 2782 2857 4.434 .226 .203 .193 .225 2.121 80 377 .204 .77 100 2510 9400 43 53 91 101 0 1344 396 948 .418 1291 894 2.394 .377 -1.26 -1.408
5 370 368 101 220 269 148 302 333 124 238 201 113 0 0 258 170 101 110 70 50 50 25 417 314 1.818 .55 .562 .708 .594 3.142 80 351 .605 .52 100 2660 9410 44 54 106 116 0 681 407 274 1.019 617 209 .981 1.041 .027 .058
6 6119 1570 101 205 6018 1365 5361 1342 112 221 5260 1137 0 0 3244 777 60 94 100 98 100 96 7383 6397 4.409 .227 .216 .224 .237 1.708 80 379 .214 .92 100 2820 9400 43 53 122 132 0 2907 380 2528 .42 2485 2106 2.381 .4 -1.251 -1.321
7 176 389 112 205 64 184 147 344 151 229 35 139 0 0 128 202 307 128 3 51 1 30 248 174 .348 2.875 3.971 1.745 1.653 3.482 80 380 4.651 .31 100 2970 9410 44 54 137 147 0 720 380 341 5.324 637 257 .188 7.354 2.413 2.879
8 1860 1183 109 225 1751 958 1582 870 151 248 1473 645 0 0 1496 819 302 139 91 96 70 91 2709 2118 1.828 .547 .438 .575 .593 2.058 80 394 .51 .89 100 3150 9410 44 54 155 165 0 2191 417 1774 1.013 1611 1194 .987 .811 .019 -.302
9 347 662 107 221 240 441 318 591 115 258 211 370 0 0 178 317 59 285 86 62 71 31 681 581 .544 1.838 1.754 1.953 2.062 2.295 80 373 2.142 .75 100 3300 9410 44 54 170 180 0 1226 409 817 3.403 1094 685 .294 3.247 1.767 1.699
10 530 701 112 223 418 478 512 675 126 277 400 452 0 0 257 309 79 226 90 78 84 50 896 852 .874 1.144 1.13 1.215 1.17 1.893 32 164 1.266 .71 60 3450 9410 46 52 187 193 0 1298 413 885 2.118 1250 837 .472 2.093 1.082 1.065
11 527 630 127 248 400 382 521 653 143 285 394 405 0 0 246 236 90 150 87 78 75 56 782 799 1.047 .955 1.028 .996 1.014 2.38 32 148 1.125 .71 60 3620 9390 44 50 204 210 0 1167 459 707 1.769 1209 750 .565 1.904 .823 .929
12 563 874 153 297 410 577 560 912 165 310 407 615 0 0 160 158 79 137 100 100 100 91 987 1022 .711 1.407 1.511 1.456 1.265 1.569 12 86 1.486 .7 50 3780 9400 45 50 220 225 0 1619 550 1069 2.606 1689 1139 .384 2.798 1.382 1.485
13 246 589 102 249 144 340 192 381 127 336 90 132 0 0 170 787 170 752 32 5 11 2 484 222 .424 2.361 1.467 2.055 1.823 4.047 80 422 6.412 .55 100 3900 9400 43 53 230 240 -100 1091 461 630 4.372 706 244 .229 2.716 2.128 1.442
14 1470 1709 103 243 1367 1466 1271 1495 124 274 1168 1252 0 0 950 981 109 222 98 95 93 83 2833 2420 .932 1.072 1.072 1.089 1.018 1.833 80 471 1.115 .84 100 4090 9410 44 54 249 259 0 3165 450 2715 1.986 2769 2319 .504 1.985 .99 .989
15 409 667 101 237 308 430 410 656 115 261 309 419 0 0 238 282 69 122 78 87 65 78 738 728 .716 1.396 1.356 1.954 1.377 3.075 32 199 1.605 .6 70 4260 9410 45 52 267 274 0 1235 439 796 2.585 1215 776 .387 2.511 1.37 1.328
16 1121 1661 96 218 1025 1443 937 1453 104 237 841 1235 0 0 666 969 54 115 99 99 97 95 2468 2076 .71 1.408 1.468 1.378 1.435 1.88 120 571 1.474 .91 120 4400 9400 42 54 279 291 0 3076 404 2672 2.607 2691 2287 .384 2.719 1.382 1.443
17 250 443 95 206 155 237 244 366 103 227 149 160 0 0 126 255 49 153 84 53 53 28 392 309 .654 1.529 1.074 1.345 1.369 2.962 32 143 4.834 .44 60 4560 9390 44 50 298 304 0 820 381 439 2.832 678 296 .353 1.989 1.502 .992
18 188 287 102 214 86 73 149 263 135 275 47 49 0 0 152 138 131 257 26 11 12 0 159 96 1.178 .849 1.043 1.125 .89 3.292 80 433 2.159 .67 100 4750 9410 44 54 315 325 -50 531 396 135 1.572 487 91 .636 1.931 .653 .949
19 326 724 111 235 215 489 280 616 153 319 169 381 0 0 244 577 141 334 55 53 36 28 704 550 .44 2.274 2.254 2.042 1.93 2.459 80 385 2.73 .75 100 4910 9410 44 54 331 341 -50 1341 435 906 4.212 1141 706 .237 4.175 2.074 2.062
20 163 279 101 198 62 81 137 233 113 243 36 35 0 0 104 156 63 257 36 12 18 2 143 71 .765 1.306 .972 1.247 1.421 4.363 80 297 9.21 .28 100 5070 9410 44 54 347 357 -50 517 367 150 2.419 431 65 .413 1.8 1.275 .848

Total number of rows: 37632

Table truncated, full table size 8463 Kbytes.




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