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Sample GSM91834 Query DataSets for GSM91834
Status Public on Jan 11, 2006
Title "083 Day11 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 Day11 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "083 Day11 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/2001-10/21416.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 1497 1015 179 445 1318 570 1256 821 190 466 1077 376 0 0 992 526 78 146 100 75 98 60 1888 1453 2.312 .432 .349 .379 .445 2.045 80 536 .434 .83 110 1850 9860 36 47 42 53 0 730 320 410 .311 591 271 3.214 .251 -1.684 -1.993
2 496 1196 210 540 286 656 467 1212 227 583 257 672 0 0 185 379 96 229 90 84 71 71 942 929 .436 2.294 2.615 2.119 2.213 2.319 32 141 3.405 .56 60 2010 9890 42 48 61 67 0 860 388 472 1.65 872 483 .606 1.881 .723 .912
3 2121 3835 176 481 1945 3354 2143 4054 186 498 1967 3573 0 0 983 1713 79 139 100 98 100 98 5299 5540 .58 1.724 1.816 1.708 1.788 1.631 80 395 1.81 .92 100 2170 9860 37 47 75 85 0 2759 346 2413 1.241 2917 2571 .806 1.307 .311 .386
4 3794 2162 181 510 3613 1652 3716 2229 188 527 3535 1719 0 0 1677 749 78 138 100 98 100 96 5265 5254 2.187 .457 .486 .457 .429 1.546 80 418 .429 .92 110 2330 9860 36 47 90 101 0 1555 367 1188 .329 1604 1237 3.04 .35 -1.604 -1.515
5 817 1334 208 571 609 763 711 1315 228 595 503 744 0 0 434 476 128 178 90 87 81 71 1372 1247 .798 1.253 1.479 1.137 1.089 2.427 32 216 1.271 .75 70 2470 9870 39 46 106 113 0 960 411 549 .901 946 535 1.109 1.064 -.15 .09
6 6353 2940 195 603 6158 2337 6069 3072 208 613 5874 2469 0 0 2747 1100 91 160 100 100 100 97 8495 8343 2.635 .38 .42 .361 .385 1.618 80 509 .376 .93 110 2640 9850 35 46 121 132 0 2115 434 1681 .273 2210 1776 3.663 .302 -1.873 -1.726
7 304 898 190 584 114 314 249 772 234 579 59 188 0 0 178 432 295 218 15 42 2 23 428 247 .363 2.754 3.186 2.745 2.494 2.272 80 419 3.25 .66 100 2820 9850 36 46 140 150 -50 646 420 226 1.982 555 135 .505 2.292 .987 1.197
8 1889 1424 110 200 1779 1224 1460 1140 196 372 1350 940 0 0 1670 1017 450 361 68 84 59 62 3003 2290 1.453 .688 .696 .893 .85 2.85 32 172 .674 .88 70 2920 9870 39 46 151 158 -100 1024 144 881 .495 820 676 2.02 .501 -1.015 -.997
9 301 1193 114 430 187 763 262 841 135 400 148 411 0 0 194 910 106 321 57 57 35 33 950 559 .245 4.08 2.777 3.418 3.279 2.727 80 429 5.15 .8 100 3130 9850 36 46 171 181 -50 858 309 549 2.935 605 296 .341 1.998 1.554 .998
10 483 1643 215 673 268 970 496 1522 220 693 281 849 0 0 159 465 96 175 84 100 75 93 1238 1130 .276 3.619 3.021 3.476 3.462 2.15 32 140 4.947 .58 60 3250 9880 41 47 185 191 0 1182 484 698 2.604 1095 611 .384 2.174 1.381 1.12
11 715 1478 205 710 510 768 679 1435 231 717 474 725 0 0 332 588 124 166 90 84 71 68 1278 1199 .664 1.506 1.53 1.396 1.518 2.075 32 232 1.896 .78 70 3410 9870 39 46 200 207 0 1063 511 553 1.083 1032 522 .923 1.1 .116 .138
12 654 1946 233 872 421 1074 691 1962 258 890 458 1090 0 0 152 304 120 246 91 100 83 91 1495 1548 .392 2.551 2.38 2.715 2.524 1.467 12 98 3.113 .74 50 3570 9850 38 43 217 222 0 1400 627 773 1.835 1412 784 .545 1.712 .876 .776
13 385 1198 226 797 159 401 354 1081 235 822 128 284 0 0 186 451 95 199 57 53 35 42 560 412 .397 2.522 2.219 2.2 2.385 2.709 80 392 3.371 .58 100 3760 9850 36 46 234 244 -50 862 573 288 1.814 778 204 .551 1.596 .859 .675
14 2134 4174 223 812 1911 3362 1772 3750 236 838 1549 2938 0 0 1182 2007 94 215 100 100 100 98 5273 4487 .568 1.759 1.897 1.729 1.668 1.518 80 464 1.831 .91 110 3880 9850 35 46 245 256 0 3003 584 2419 1.266 2698 2114 .79 1.365 .34 .448
15 546 1773 269 855 277 918 589 1991 274 909 320 1136 0 0 255 565 105 263 66 83 58 75 1195 1456 .302 3.314 3.55 2.775 2.605 1.534 12 104 4.217 .56 50 4060 9870 40 45 266 271 0 1276 615 660 2.384 1432 817 .419 2.554 1.254 1.353
16 1549 3884 226 817 1323 3067 1392 2987 260 865 1166 2170 0 0 982 2369 558 490 71 93 51 73 4390 3336 .431 2.318 1.861 2.222 2.111 1.771 80 470 2.457 .9 110 4200 9860 36 47 277 288 0 2794 588 2206 1.668 2149 1561 .6 1.339 .738 .421
17 333 1019 220 792 113 227 249 893 261 841 29 101 0 0 397 537 605 604 3 12 1 5 340 130 .498 2.009 3.483 1.89 1.801 3.429 80 400 .859 .86 100 4390 9850 36 46 297 307 -50 733 570 163 1.445 642 73 .692 2.506 .531 1.325
18 330 968 227 831 103 137 264 927 232 838 37 96 0 0 172 322 84 193 36 37 27 17 240 133 .752 1.33 2.595 2.906 2.695 4.582 80 329 3.667 .4 100 4540 9850 36 46 312 322 -50 696 598 99 .957 667 69 1.045 1.867 -.064 .9
19 888 3535 226 847 662 2688 807 3200 238 916 581 2353 0 0 426 1649 103 464 92 96 90 90 3350 2934 .246 4.06 4.05 4.191 3.905 2.091 80 418 4.133 .89 110 4670 9860 36 47 324 335 0 2543 609 1934 2.921 2302 1693 .342 2.914 1.547 1.543
20 550 1941 268 990 282 951 578 1859 276 1007 310 869 0 0 242 334 100 264 66 100 66 91 1233 1179 .297 3.372 2.803 4.579 3.427 3.77 12 98 4.289 .52 50 4830 9850 38 43 343 348 0 1396 712 684 2.426 1337 625 .412 2.017 1.279 1.012

Total number of rows: 37632

Table truncated, full table size 8735 Kbytes.




Supplementary data files not provided
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