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Sample GSM91727 Query DataSets for GSM91727
Status Public on Jan 11, 2006
Title "409 Day8 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 Day8 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "409 Day8 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/2001-10/21437.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 1375 898 149 381 1226 517 1108 768 166 401 959 387 0 0 1006 499 84 155 97 75 92 57 1743 1346 2.371 .422 .404 .437 .464 2.283 80 392 .446 .86 100 1740 9150 63 73 44 54 0 1182 501 680 .555 1011 509 1.802 .531 -.85 -.913
2 220 445 158 408 62 37 197 417 182 469 39 9 0 0 118 176 110 282 31 8 12 1 99 48 1.676 .597 .231 1.177 1.592 4.652 80 404 5.04 .35 100 1950 9160 64 74 65 75 -50 586 537 49 .785 549 12 1.274 .304 -.349 -1.72
3 1558 1677 162 456 1396 1221 1485 1429 174 506 1323 973 0 0 797 847 82 268 98 88 94 80 2617 2296 1.143 .875 .735 .824 .888 1.466 52 270 .948 .89 90 2070 9140 62 71 77 86 0 2207 600 1607 1.151 1880 1280 .869 .968 .203 -.047
4 3072 1033 152 410 2920 623 2694 949 164 431 2542 539 0 0 1977 527 75 139 100 85 100 72 3543 3081 4.687 .213 .212 .205 .219 1.876 80 487 .209 .87 110 2220 9150 62 73 91 102 0 1359 539 820 .281 1249 709 3.562 .279 -1.833 -1.842
5 352 579 156 432 196 147 242 474 163 454 86 42 0 0 319 284 68 148 53 30 41 20 343 128 1.333 .75 .488 1.214 .942 4.989 80 354 1.019 .73 100 2420 9160 64 74 112 122 -50 762 568 193 .987 624 55 1.013 .643 -.019 -.638
6 5839 2236 151 432 5688 1804 5018 1926 156 452 4867 1494 0 0 3382 1174 57 145 100 95 100 92 7492 6361 3.153 .317 .307 .291 .306 1.913 80 383 .303 .91 100 2530 9150 63 73 123 133 0 2942 568 2374 .417 2534 1966 2.396 .404 -1.261 -1.308
7 221 499 147 425 74 74 190 459 153 445 43 34 0 0 149 264 62 141 40 23 20 16 148 77 1 1 .791 1.894 1.669 3.896 80 363 2.677 .57 100 2730 9160 64 74 143 153 -50 657 559 97 1.316 604 45 .76 1.04 .396 .057
8 2318 1168 150 414 2168 754 1581 906 154 429 1431 492 0 0 2052 812 63 128 98 76 97 63 2922 1923 2.875 .348 .344 .336 .363 1.743 80 387 .354 .91 110 2860 9140 61 72 155 166 0 1537 545 992 .458 1192 647 2.185 .452 -1.128 -1.144
9 407 894 154 433 253 461 361 846 166 443 207 413 0 0 202 397 77 135 80 78 61 71 714 620 .549 1.822 1.995 2.077 1.984 2.123 52 335 2.333 .73 90 3000 9160 64 73 170 179 0 1176 570 607 2.398 1113 543 .417 2.625 1.262 1.392
10 324 575 147 358 177 217 230 453 162 378 83 95 0 0 228 340 77 130 51 43 42 32 394 178 .816 1.226 1.145 1.648 1.689 2.629 80 450 1.671 .75 100 3200 9160 64 74 190 200 -50 757 471 286 1.613 596 125 .62 1.506 .69 .591
11 997 876 207 355 790 521 1002 899 243 370 795 544 0 0 209 175 127 132 100 100 100 91 1311 1339 1.516 .659 .684 .637 .67 1.59 12 86 .792 .79 50 3330 9140 64 69 205 210 0 1153 467 686 .868 1183 716 1.152 .9 -.205 -.151
12 272 409 137 303 135 106 238 335 155 322 101 32 0 0 151 196 84 141 55 33 33 21 241 133 1.274 .785 .317 .782 1.039 3.174 80 430 1.569 .61 100 3520 9150 63 73 222 232 -50 538 399 139 1.033 441 42 .968 .417 .047 -1.262
13 275 425 135 273 140 152 224 354 145 286 89 81 0 0 161 189 63 97 60 46 41 32 292 170 .921 1.086 .91 1.237 1.063 3.69 80 370 1.618 .46 100 3680 9150 63 73 238 248 -50 559 359 200 1.429 466 107 .7 1.198 .515 .26
14 1676 1960 136 276 1540 1684 1256 1636 145 286 1120 1360 0 0 1335 1429 62 99 98 93 95 88 3224 2480 .914 1.094 1.214 1.064 1.061 1.875 80 469 1.103 .93 110 3820 9140 61 72 251 262 0 2579 363 2216 1.439 2153 1789 .695 1.598 .525 .676
15 726 1043 153 318 573 725 758 1050 173 331 605 732 0 0 208 243 85 116 100 100 100 100 1298 1337 .79 1.265 1.21 1.294 1.179 1.345 12 98 1.415 .89 50 3990 9140 64 69 271 276 0 1372 418 954 1.665 1382 963 .601 1.592 .735 .671
16 2000 3877 136 284 1864 3593 1521 3052 145 299 1385 2768 0 0 1332 2527 61 109 100 100 100 100 5457 4153 .519 1.928 1.999 1.934 1.919 1.329 80 510 1.941 .96 110 4130 9140 61 72 282 293 0 5101 374 4728 2.536 4016 3642 .394 2.63 1.343 1.395
17 383 531 159 302 224 229 375 508 173 323 216 206 0 0 127 122 72 127 83 83 75 41 453 422 .978 1.022 .954 1.174 1.013 1.516 12 90 1.637 .59 50 4280 9130 63 68 300 305 0 699 397 301 1.345 668 271 .743 1.255 .428 .328
18 271 410 139 286 132 124 228 378 149 304 89 92 0 0 175 174 62 115 60 43 33 26 256 181 1.065 .939 1.034 1.126 1.03 2.678 80 382 1.379 .46 100 4460 9150 63 73 316 326 -50 539 376 163 1.236 497 121 .809 1.36 .306 .444
19 647 1351 135 276 512 1075 541 1209 144 297 406 933 0 0 297 667 63 117 97 96 92 93 1587 1339 .476 2.1 2.298 1.974 2.122 1.843 80 449 2.265 .9 110 4590 9140 61 72 328 339 0 1778 363 1414 2.763 1591 1228 .362 3.024 1.466 1.596
20 220 328 138 270 82 58 180 321 141 284 42 51 0 0 145 156 55 95 37 33 28 17 140 93 1.414 .707 1.214 1.355 1.354 2.865 80 358 1.391 .39 100 4780 9140 62 72 348 358 -50 432 355 76 .931 422 67 1.074 1.598 -.104 .676

Total number of rows: 37632

Table truncated, full table size 8473 Kbytes.




Supplementary data files not provided
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