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Sample GSM91707 Query DataSets for GSM91707
Status Public on Jan 11, 2006
Title "003 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 "003 Day8 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "003 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/2001-10/21430.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 2097 1107 246 535 1851 572 1507 897 277 556 1261 362 0 0 1836 753 226 186 90 70 71 48 2423 1623 3.236 .309 .287 .394 .379 2.261 80 398 .34 .86 100 1860 9430 30 40 26 36 0 1153 557 596 .322 934 377 3.107 .299 -1.635 -1.742
2 490 1107 257 626 233 481 386 1069 296 739 129 443 0 0 322 535 245 409 31 51 16 27 714 572 .484 2.064 3.434 2.545 1.952 3.513 80 353 3.589 .45 100 2050 9450 32 42 45 55 -100 1153 652 501 2.15 1114 461 .465 3.577 1.105 1.839
3 2450 2460 296 618 2154 1842 1881 2029 423 812 1585 1411 0 0 1832 1470 526 531 86 86 71 63 3996 2996 1.169 .855 .89 .98 .875 2.182 52 228 .717 .89 80 2160 9430 31 39 57 65 -100 2563 644 1919 .891 2114 1470 1.123 .927 -.167 -.109
4 4468 1313 226 406 4242 907 4038 1096 299 460 3812 690 0 0 2887 757 384 287 98 76 93 58 5149 4502 4.677 .214 .181 .189 .217 1.726 80 463 .226 .89 100 2340 9440 31 41 74 84 0 1368 423 945 .223 1142 719 4.49 .189 -2.167 -2.407
5 739 688 226 384 513 304 508 561 255 408 282 177 0 0 701 445 211 154 56 53 33 38 817 459 1.688 .593 .628 .679 .667 2.49 80 386 .625 .82 100 2520 9450 32 42 92 102 -50 717 400 317 .617 584 184 1.62 .654 -.696 -.613
6 10171 3731 219 359 9952 3372 7984 2706 225 370 7765 2347 0 0 7015 2746 83 133 98 97 97 95 13324 10112 2.951 .339 .302 .316 .314 1.47 80 380 .345 .95 100 2660 9440 31 41 106 116 0 3886 374 3513 .353 2819 2445 2.833 .315 -1.502 -1.667
7 363 538 213 356 150 182 283 404 240 370 70 48 0 0 281 615 200 132 26 27 13 20 332 118 .824 1.213 .686 1.058 .93 3.826 80 358 3 .54 100 2840 9450 32 42 124 134 -50 560 371 190 1.264 421 50 .791 .714 .338 -.485
8 3880 1501 213 355 3667 1146 2829 1079 271 390 2616 724 0 0 3609 1204 421 199 81 77 75 65 4813 3340 3.2 .313 .277 .342 .319 2.803 80 419 .312 .95 110 2960 9430 29 40 135 146 0 1564 370 1194 .326 1124 754 3.072 .288 -1.619 -1.794
9 684 1602 229 354 455 1248 648 1528 298 404 419 1174 0 0 412 840 452 219 50 86 7 82 1703 1593 .365 2.743 2.802 2.715 2.734 1.998 52 359 2.514 .87 90 3130 9460 33 42 153 162 0 1669 369 1300 2.857 1592 1223 .35 2.919 1.515 1.545
10 944 1469 218 346 726 1123 1053 1587 231 373 835 1241 0 0 517 760 105 162 81 78 81 75 1849 2076 .646 1.547 1.486 1.452 1.671 1.946 32 160 1.578 .89 60 3300 9440 33 39 172 178 0 1530 360 1170 1.611 1653 1293 .621 1.548 .688 .631
11 1265 1253 234 385 1031 868 1258 1151 261 391 1024 766 0 0 665 610 130 138 90 87 84 87 1899 1790 1.188 .842 .748 .904 .859 1.725 32 164 .934 .9 60 3470 9460 35 41 189 195 0 1305 401 904 .877 1199 798 1.14 .779 -.189 -.36
12 436 763 223 380 213 383 316 498 248 407 93 118 0 0 359 568 129 156 41 47 25 36 596 211 .556 1.798 1.269 1.463 1.423 2.716 80 478 1.81 .81 100 3630 9450 32 42 203 213 -50 795 396 399 1.873 519 123 .534 1.322 .905 .402
13 920 1559 254 449 666 1110 1074 1448 303 504 820 999 0 0 518 849 217 301 75 81 62 62 1776 1819 .6 1.667 1.218 1.593 1.48 3.214 32 159 1.773 .83 60 3800 9450 34 40 222 228 0 1624 468 1156 1.736 1508 1041 .576 1.269 .796 .344
14 3234 3890 223 422 3011 3468 2070 2570 274 488 1847 2148 0 0 2707 2959 241 295 90 90 88 90 6479 3995 .868 1.152 1.163 1.181 1.196 1.346 52 279 1.117 .97 80 3930 9430 31 39 234 242 0 4052 440 3613 1.2 2677 2238 .833 1.211 .263 .277
15 1111 2018 322 626 789 1392 1152 2226 354 662 830 1600 0 0 450 500 192 294 91 100 83 91 2181 2430 .567 1.764 1.928 1.744 1.701 1.559 12 80 1.616 .89 50 4090 9430 32 37 251 256 0 2102 652 1450 1.838 2319 1667 .544 2.008 .878 1.006
16 2339 4037 209 442 2130 3595 1595 2529 231 479 1386 2087 0 0 2084 3759 118 204 95 95 95 92 5725 3473 .592 1.688 1.506 1.57 1.656 1.486 80 398 1.779 .97 100 4240 9440 31 41 264 274 0 4205 460 3745 1.758 2634 2174 .569 1.569 .814 .649
17 417 673 208 471 209 202 291 586 225 478 83 115 0 0 321 371 107 162 45 41 32 23 411 198 1.035 .967 1.386 1.515 1.228 4.348 80 382 1.335 .72 100 4410 9460 33 43 281 291 -50 701 491 210 1.007 610 120 .993 1.443 .01 .529
18 389 596 221 485 168 111 283 485 228 495 62 0 0 0 306 322 86 167 42 28 32 21 279 62 1.514 .661 null 1.37 1.278 3.464 80 326 1.402 .54 100 4570 9460 33 43 297 307 -50 621 505 116 .688 505 0 1.453 null -.539 null
19 1042 2753 226 555 816 2198 891 2315 234 580 665 1760 0 0 566 1619 87 215 95 95 91 91 3014 2425 .371 2.694 2.647 2.33 2.545 1.987 80 406 2.905 .93 110 4700 9440 30 41 309 320 0 2868 578 2290 2.806 2411 1833 .356 2.757 1.488 1.463
20 419 857 234 589 185 268 348 819 244 640 114 230 0 0 257 403 86 251 52 50 41 26 453 344 .69 1.449 2.018 1.397 1.587 3.289 80 353 2.843 .52 100 4880 9460 33 43 328 338 -50 893 614 279 1.509 853 240 .663 2.102 .594 1.071

Total number of rows: 37632

Table truncated, full table size 8604 Kbytes.




Supplementary data files not provided
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