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Sample GSM91713 Query DataSets for GSM91713
Status Public on Jan 11, 2006
Title "409 Day0 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 Day0 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "409 Day0 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/2001-10/21432.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 1767 1249 208 745 1559 504 1360 956 280 770 1152 211 0 0 1330 717 287 216 84 50 67 36 2063 1363 3.093 .323 .183 .294 .376 3.4 52 213 .43 .83 80 1890 9770 43 51 40 48 0 991 591 400 .257 759 167 3.898 .145 -1.963 -2.782
2 349 894 196 719 153 175 296 774 233 733 100 55 0 0 246 483 201 198 27 31 16 22 328 155 .874 1.144 .55 1.689 1.871 2.958 80 427 2.152 .67 100 2100 9780 43 53 60 70 -50 710 571 139 .908 614 44 1.102 .437 -.14 -1.196
3 1912 2459 198 690 1714 1769 1597 1952 297 739 1399 1262 0 0 1095 1335 430 232 88 92 75 88 3483 2661 .969 1.032 .902 .941 1.005 1.846 52 285 1.127 .92 90 2230 9750 40 49 73 82 0 1952 548 1404 .819 1549 1002 1.221 .716 -.288 -.482
4 3585 1448 202 743 3383 705 2924 1252 290 835 2722 509 0 0 2142 769 421 335 92 57 86 48 4088 3231 4.799 .208 .187 .186 .221 2.016 52 302 .244 .83 90 2390 9760 41 50 89 98 0 1149 590 560 .165 994 404 6.046 .148 -2.596 -2.752
5 460 1649 209 905 251 744 331 1740 247 1020 122 835 0 0 363 618 201 432 36 73 21 50 995 957 .337 2.964 6.844 4.117 4.321 3.674 80 392 4.032 .47 100 2530 9740 39 49 103 113 -100 1309 718 590 2.352 1381 663 .425 5.432 1.234 2.441
6 6022 2725 186 685 5836 2040 5101 2274 200 698 4915 1589 0 0 4579 1849 91 199 98 85 98 80 7876 6504 2.861 .35 .323 .325 .354 1.641 80 480 .36 .94 110 2700 9760 40 51 119 130 0 2163 544 1619 .277 1805 1261 3.605 .257 -1.85 -1.962
7 251 698 193 653 58 45 221 655 357 689 28 2 0 0 150 309 621 296 0 22 0 3 103 30 1.289 .776 .071 2.678 2.66 3.285 80 419 .435 .64 100 2880 9780 43 53 138 148 -50 554 518 36 .616 520 2 1.624 .057 -.7 -4.141
8 118 223 149 525 -31 -302 80 207 319 576 -69 -318 0 0 168 121 654 410 2 0 0 0 -333 -387 null null null 4.435 4.239 2.273 80 355 .478 .85 100 3040 9780 43 53 154 164 -50 177 417 -240 null 164 null null null null null
9 458 1727 168 672 290 1055 432 1532 170 628 264 860 0 0 297 1053 94 295 65 68 53 56 1345 1124 .275 3.638 3.258 3.904 3.91 2.09 80 349 4.027 .88 100 3190 9780 43 53 169 179 -50 1371 533 837 2.887 1216 683 .346 2.585 1.53 1.37
10 402 1152 199 710 203 442 295 915 239 768 96 205 0 0 309 757 199 388 35 32 20 22 645 301 .459 2.177 2.135 2.364 2.52 3.26 80 438 2.829 .8 100 3350 9780 43 53 185 195 -50 914 563 351 1.728 726 163 .579 1.695 .789 .761
11 1371 1873 248 731 1123 1142 1446 2006 271 769 1198 1275 0 0 421 652 131 229 100 91 100 83 2265 2473 .983 1.017 1.064 1.022 .93 1.417 12 90 1.347 .88 50 3500 9760 43 48 202 207 0 1487 580 906 .807 1592 1012 1.239 .845 -.309 -.244
12 330 947 182 649 148 298 251 786 198 663 69 137 0 0 210 552 94 186 41 42 31 32 446 206 .497 2.014 1.986 2.583 2.395 3.544 80 456 3.262 .71 100 3660 9780 43 53 216 226 -50 752 515 237 1.598 624 109 .626 1.576 .676 .656
13 686 1709 231 717 455 992 690 1698 247 711 459 981 0 0 222 337 96 186 91 100 91 100 1447 1440 .459 2.18 2.137 2.48 2.456 2.226 12 85 2.606 .77 50 3820 9760 43 48 234 239 0 1356 569 787 1.73 1348 779 .578 1.696 .791 .762
14 1770 2785 169 612 1601 2173 1496 2443 184 622 1327 1831 0 0 1298 1799 73 172 95 92 90 88 3774 3158 .737 1.357 1.38 1.372 1.354 1.885 120 526 1.411 .93 120 3960 9770 41 53 245 257 0 2210 486 1725 1.077 1939 1453 .928 1.095 .107 .131
15 467 1159 187 643 280 516 342 1010 197 673 155 367 0 0 394 753 73 191 66 60 51 48 796 522 .543 1.843 2.368 2.467 2.124 2.374 80 326 2.161 .82 100 4130 9770 42 52 263 273 -50 920 510 410 1.463 802 291 .684 1.879 .549 .91
16 1462 2771 194 691 1268 2080 960 1859 201 723 766 1168 0 0 1333 2411 75 190 94 89 91 80 3348 1934 .61 1.64 1.525 1.534 1.518 1.857 120 477 1.8 .94 120 4270 9760 40 52 276 288 0 2199 548 1651 1.302 1475 927 .768 1.21 .381 .275
17 302 875 181 623 121 252 238 780 195 643 57 157 0 0 196 434 80 184 45 42 27 25 373 214 .48 2.083 2.754 2.556 2.435 2.63 80 374 3.112 .65 100 4440 9770 42 52 294 304 -50 694 494 200 1.653 619 125 .605 2.186 .725 1.128
18 291 648 168 540 123 108 221 575 179 553 53 35 0 0 200 324 65 138 43 31 28 16 231 88 1.139 .878 .66 2.236 2.56 3.097 80 323 2.033 .66 100 4600 9770 42 52 310 320 -50 514 429 86 .697 456 28 1.435 .524 -.521 -.932
19 703 1677 166 591 537 1086 622 1480 183 627 456 889 0 0 394 885 90 201 93 87 83 76 1623 1345 .494 2.022 1.95 1.97 2.034 1.73 120 503 2.32 .88 120 4730 9760 40 52 322 334 0 1331 469 862 1.605 1175 706 .623 1.547 .683 .63
20 337 873 184 683 153 190 270 774 190 698 86 91 0 0 229 449 67 167 51 45 42 30 343 177 .805 1.242 1.058 2.282 2.102 2.324 80 362 2.532 .68 100 4910 9770 42 52 341 351 -50 693 542 151 .986 614 72 1.015 .84 -.021 -.252

Total number of rows: 37632

Table truncated, full table size 8593 Kbytes.




Supplementary data files not provided
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