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Sample GSM91718 Query DataSets for GSM91718
Status Public on Jan 11, 2006
Title "57-394 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 "57-394 Day0 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "57-394 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/2001-10/21507.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 1721 1142 126 440 1595 702 1351 1145 179 473 1225 705 0 0 1174 593 206 230 92 75 86 65 2297 1930 2.272 .44 .576 .478 .483 1.746 52 254 .452 .82 80 1760 9090 25 33 55 63 0 1360 524 836 .524 1363 839 1.909 .685 -.932 -.546
2 254 714 130 468 124 246 168 500 186 558 38 32 0 0 311 642 358 743 11 13 3 3 370 70 .504 1.984 .842 2.677 3.125 3.157 80 386 10.112 .82 100 1930 9110 26 36 71 81 -50 850 557 293 2.362 595 38 .423 1.003 1.24 .004
3 1602 1989 119 471 1483 1518 1104 1669 145 510 985 1198 0 0 1261 1314 133 247 92 80 90 71 3001 2183 .977 1.024 1.216 .951 .995 2.035 52 282 1.033 .88 90 2060 9080 23 32 84 93 0 2368 561 1807 1.219 1987 1426 .821 1.448 .285 .534
4 2853 1416 120 442 2733 974 2381 1360 237 834 2261 918 0 0 1879 697 1400 4172 71 0 42 0 3707 3179 2.806 .356 .406 .401 .335 2.293 52 359 .331 .83 90 2210 9090 24 33 99 108 0 1686 526 1160 .424 1619 1093 2.357 .483 -1.237 -1.049
5 1144 1348 135 567 1009 781 1201 1223 199 565 1066 656 0 0 638 685 151 242 91 83 83 66 1790 1722 1.292 .774 .615 .641 .719 1.796 12 80 .873 .78 50 2380 9080 25 30 118 123 0 1605 675 930 .921 1456 781 1.085 .733 -.118 -.449
6 6573 2396 109 411 6464 1985 4658 1803 131 450 4549 1392 0 0 5766 1811 86 220 98 86 97 81 8449 5941 3.256 .307 .306 .298 .296 1.65 80 439 .294 .94 100 2520 9080 23 33 130 140 0 2852 489 2363 .366 2146 1657 2.735 .364 -1.452 -1.457
7 160 538 116 450 44 88 131 493 198 541 15 43 0 0 121 313 355 762 6 3 0 0 132 58 .5 2 2.867 4.927 5.379 3.708 80 397 2.652 .48 100 2720 9110 26 36 150 160 -50 640 536 105 2.381 587 51 .42 3.413 1.252 1.771
8 2465 1517 117 490 2348 1027 1599 1352 204 530 1482 862 0 0 1987 889 378 259 86 76 76 65 3375 2344 2.286 .437 .582 .493 .471 2.349 52 287 .421 .86 90 2860 9080 23 32 164 173 0 1806 583 1223 .521 1610 1026 1.92 .692 -.941 -.53
9 401 1034 121 421 280 613 465 1062 137 459 344 641 0 0 221 377 74 238 78 84 68 59 893 985 .457 2.189 1.863 2.115 1.906 2.202 32 186 3.24 .57 70 2990 9080 24 31 178 185 0 1231 501 730 2.606 1264 763 .384 2.218 1.382 1.149
10 251 557 127 462 124 95 153 470 211 704 26 8 0 0 238 297 538 2493 10 0 0 0 219 34 1.305 .766 .308 1.997 2.131 3.475 80 468 2.498 .69 100 3190 9110 26 36 197 207 -50 663 550 113 .912 560 10 1.096 .366 -.133 -1.449
11 720 1345 152 414 568 931 701 1434 175 506 549 1020 0 0 316 497 98 274 91 91 83 75 1499 1569 .61 1.639 1.858 2.099 1.884 1.672 12 86 1.815 .77 50 3320 9090 26 31 212 217 0 1601 493 1108 1.951 1707 1214 .512 2.212 .964 1.145
12 386 1058 115 411 271 647 352 1077 153 496 237 666 0 0 193 495 243 325 50 68 9 50 918 903 .419 2.387 2.81 2.647 2.835 2.19 32 148 3.623 .66 60 3480 9090 26 32 228 234 0 1260 489 770 2.842 1282 793 .352 3.345 1.507 1.742
13 233 572 114 401 119 171 188 517 163 480 74 116 0 0 156 274 430 503 5 10 0 0 290 190 .696 1.437 1.568 2.046 2.042 3.554 80 406 4.02 .47 100 3660 9110 26 36 244 254 -50 681 477 204 1.711 615 138 .585 1.866 .775 .9
14 1192 1422 110 401 1082 1021 824 1027 120 449 714 626 0 0 1244 1064 60 220 90 75 83 64 2103 1340 1.06 .944 .877 1.03 .955 2.9 120 587 .895 .85 130 3800 9090 22 35 256 269 -100 1693 477 1215 1.123 1223 745 .89 1.044 .168 .062
15 291 673 120 405 171 268 182 534 153 476 62 129 0 0 263 430 158 313 30 31 22 18 439 191 .638 1.567 2.081 2.429 2.329 3.505 80 397 2.157 .64 100 3970 9110 26 36 275 285 -50 801 482 319 1.866 636 154 .536 2.477 .9 1.309
16 1622 3026 119 440 1503 2586 997 2182 146 495 878 1742 0 0 1621 2468 143 305 80 85 73 77 4089 2620 .581 1.721 1.984 2.15 1.73 2.738 80 503 1.68 .9 110 4130 9090 23 34 290 301 -100 3602 524 3079 2.048 2598 2074 .488 2.362 1.034 1.24
17 532 997 123 530 409 467 554 925 134 573 431 395 0 0 124 337 73 263 100 83 100 16 876 826 .876 1.142 .916 1.004 1.066 1.875 12 80 3.103 .48 50 4280 9080 25 30 308 313 0 1187 631 556 1.359 1101 470 .736 1.091 .443 .126
18 469 974 128 406 341 568 487 1050 134 435 359 644 0 0 166 255 60 191 100 83 83 75 909 1003 .6 1.666 1.794 1.61 1.509 2.302 12 72 2.097 .61 50 4420 9070 24 29 322 327 0 1160 483 676 1.983 1250 767 .504 2.136 .988 1.095
19 621 1187 113 417 508 770 538 1091 134 510 425 674 0 0 335 579 117 663 92 50 73 21 1278 1099 .66 1.516 1.586 1.433 1.474 2.109 80 474 1.911 .77 100 4580 9090 24 34 336 346 0 1413 496 917 1.804 1299 802 .554 1.888 .852 .917
20 582 781 124 442 458 339 584 758 167 636 460 316 0 0 128 152 205 924 100 0 58 0 797 776 1.351 .74 .687 .661 .792 1.735 12 80 1.748 .57 50 4750 9080 25 30 355 360 0 930 526 404 .881 902 376 1.135 .818 -.183 -.29

Total number of rows: 37632

Table truncated, full table size 8445 Kbytes.




Supplementary data files not provided
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