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Sample GSM91710 Query DataSets for GSM91710
Status Public on Jan 11, 2006
Title "409 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 "409 Day -4 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "409 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/2001-10/21431.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 1260 961 147 320 1113 641 880 708 158 336 733 388 0 0 1106 727 69 113 88 80 85 67 1754 1121 1.736 .576 .529 .602 .588 2.371 80 394 .602 .91 100 1870 9140 35 45 41 51 0 769 256 513 .461 566 310 2.17 .423 -1.118 -1.24
2 560 1180 185 380 375 800 513 1353 188 396 328 973 0 0 173 386 91 157 100 91 91 83 1175 1301 .469 2.133 2.966 2.277 2.263 1.482 12 80 2.44 .81 50 2030 9140 37 42 59 64 0 944 304 640 1.707 1082 778 .586 2.373 .771 1.247
3 1631 2401 148 299 1483 2102 1298 1719 202 368 1150 1420 0 0 1017 1665 240 316 94 92 90 84 3585 2570 .706 1.417 1.235 1.252 1.277 1.919 52 313 1.576 .86 90 2170 9130 34 43 71 80 0 1921 239 1682 1.134 1375 1136 .882 .988 .181 -.018
4 2751 1025 150 300 2601 725 2381 830 211 365 2231 530 0 0 2121 668 305 290 87 71 80 46 3326 2761 3.588 .279 .238 .271 .291 1.846 80 409 .29 .87 100 2330 9130 34 44 87 97 0 820 240 580 .223 664 424 4.484 .19 -2.165 -2.396
5 480 646 148 300 332 346 349 478 179 324 201 178 0 0 436 475 246 134 45 60 20 38 678 379 .96 1.042 .886 1.013 .976 2.67 80 344 1.123 .83 100 2520 9160 37 47 106 116 -50 517 240 277 .834 382 142 1.199 .708 -.262 -.497
6 6534 3471 140 296 6394 3175 5496 3161 155 321 5356 2865 0 0 4405 2160 100 198 95 96 95 93 9569 8221 2.014 .497 .535 .516 .499 1.764 80 432 .479 .94 110 2650 9150 35 46 118 129 0 2777 237 2540 .397 2529 2292 2.517 .428 -1.332 -1.225
7 217 399 149 289 68 110 185 318 163 307 36 29 0 0 166 276 138 132 18 27 7 16 178 65 .618 1.618 .806 1.568 1.575 4.628 80 334 2.379 .59 100 2830 9160 37 47 137 147 -50 319 231 88 1.294 254 23 .773 .644 .372 -.634
8 2074 1221 153 303 1921 918 1461 797 156 328 1308 494 0 0 2040 1108 60 138 92 82 86 63 2839 1802 2.093 .478 .378 .501 .518 2.815 120 449 .492 .91 120 2970 9150 35 47 150 162 0 977 242 734 .382 638 395 2.616 .302 -1.387 -1.727
9 461 1573 143 319 318 1254 371 1263 157 351 228 944 0 0 299 1061 74 156 76 86 63 82 1572 1172 .254 3.943 4.14 4.095 3.927 2.392 52 314 4.147 .86 90 3120 9170 38 47 166 175 0 1258 255 1003 3.155 1010 755 .317 3.312 1.658 1.728
10 458 1063 147 316 311 747 320 767 167 336 173 451 0 0 355 825 87 137 67 77 48 66 1058 624 .416 2.402 2.607 2.303 2.166 2.46 80 427 2.601 .86 100 3280 9150 36 46 182 192 0 850 253 598 1.922 614 361 .52 2.086 .942 1.06
11 973 1298 164 336 809 962 1033 1340 186 353 869 1004 0 0 595 670 98 134 81 81 78 81 1771 1873 .841 1.189 1.155 1.093 1.2 2.636 32 160 1.201 .91 60 3450 9160 39 45 201 207 0 1038 269 770 .951 1072 803 1.051 .924 -.072 -.114
12 790 1617 180 375 610 1242 815 1773 194 386 635 1398 0 0 286 490 85 147 91 100 91 91 1852 2033 .491 2.036 2.202 2.139 1.873 2.363 12 90 2.356 .8 50 3610 9150 38 43 217 222 0 1294 300 994 1.629 1418 1118 .614 1.761 .704 .817
13 770 1507 161 364 609 1143 824 1570 187 371 663 1206 0 0 285 355 102 130 91 100 83 91 1752 1869 .533 1.877 1.819 1.708 1.711 1.991 12 78 2.171 .79 50 3770 9150 38 43 233 238 0 1206 291 914 1.501 1256 965 .666 1.455 .586 .541
14 1353 2332 142 299 1211 2033 879 1437 156 321 737 1138 0 0 1476 2513 73 121 91 92 85 89 3244 1875 .596 1.679 1.544 1.632 1.618 2.027 120 539 1.746 .94 120 3900 9150 35 47 243 255 0 1866 239 1626 1.343 1150 910 .745 1.235 .425 .305
15 401 830 155 298 246 532 221 505 166 323 66 207 0 0 381 728 73 128 46 58 40 46 778 273 .462 2.163 3.136 2.273 2.25 2.729 80 318 2.127 .86 100 4080 9170 38 48 262 272 -50 664 238 426 1.73 404 166 .578 2.509 .791 1.327
16 1365 3800 148 299 1217 3501 882 2309 156 320 734 2010 0 0 1398 4187 63 126 93 94 87 92 4718 2744 .348 2.877 2.738 2.874 2.822 2.315 120 452 3.078 .95 120 4210 9150 35 47 274 286 0 3040 239 2801 2.301 1847 1608 .435 2.191 1.203 1.131
17 272 509 152 316 120 193 189 400 158 325 37 84 0 0 205 324 70 114 37 46 25 32 313 121 .622 1.608 2.27 1.736 1.738 3.061 80 367 1.944 .69 100 4390 9170 38 48 293 303 -50 407 253 154 1.287 320 67 .777 1.816 .364 .861
18 286 462 150 318 136 144 187 354 156 337 37 36 0 0 244 331 74 138 40 30 25 17 280 73 .944 1.059 .973 1.467 1.498 3.329 80 310 1.548 .7 100 4550 9170 38 48 309 319 -50 370 254 115 .847 283 29 1.181 .778 -.239 -.361
19 551 1286 148 332 403 954 487 1014 157 359 339 682 0 0 326 777 77 180 88 90 79 80 1357 1021 .422 2.367 2.012 2.365 2.359 2.067 120 485 2.587 .87 120 4680 9150 35 47 321 333 0 1029 266 763 1.894 811 546 .528 1.609 .921 .687
20 228 435 138 337 90 98 178 365 147 356 40 28 0 0 150 257 54 139 42 27 28 17 188 68 .918 1.089 .7 1.616 1.704 3.378 80 352 2.749 .56 100 4860 9170 38 48 340 350 -50 348 270 78 .871 292 22 1.148 .56 -.199 -.837

Total number of rows: 37632

Table truncated, full table size 8511 Kbytes.




Supplementary data files not provided
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