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Sample GSM91730 Query DataSets for GSM91730
Status Public on Jan 11, 2006
Title "57-394 Day2 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 Day2 in-vivo SP Inf, PBMC 3rd TC"
Organism Homo sapiens
Characteristics "57-394 Day2 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/2001-10/21511.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 1308 1160 259 545 1049 615 1255 1080 330 662 996 535 0 0 426 306 263 650 100 41 83 0 1664 1531 1.706 .586 .537 .541 .543 1.948 12 60 1.266 .52 50 1670 9180 42 47 36 41 0 1275 599 676 .644 1187 588 1.552 .59 -.634 -.761
2 226 701 128 505 98 196 192 627 159 549 64 122 0 0 135 376 127 356 32 26 16 7 294 186 .5 2 1.906 2.23 2.331 3.354 80 419 5.451 .48 100 1830 9220 44 54 50 60 -50 770 555 215 2.198 689 134 .455 2.095 1.136 1.067
3 958 1832 121 498 837 1334 747 1527 144 538 626 1029 0 0 658 1180 100 305 86 76 80 63 2171 1655 .627 1.594 1.644 1.72 1.587 2.314 52 215 1.885 .84 80 1980 9190 42 50 66 74 0 2013 547 1466 1.751 1678 1131 .571 1.806 .809 .853
4 1613 886 109 463 1504 423 1541 797 121 479 1432 334 0 0 1047 503 64 214 97 58 90 41 1927 1766 3.556 .281 .233 .268 .268 2.882 80 384 .355 .75 100 2120 9190 41 51 79 89 0 974 509 465 .309 876 367 3.236 .256 -1.694 -1.964
5 281 589 119 486 162 103 177 488 141 534 58 2 0 0 242 314 91 340 46 23 33 6 265 60 1.573 .636 .034 1.794 2.048 4.212 80 388 1.995 .51 100 2300 9220 44 54 97 107 -50 647 534 113 .699 536 2 1.431 .038 -.517 -4.722
6 5542 1783 117 490 5425 1293 3918 1487 125 536 3801 997 0 0 4150 1060 53 268 100 82 100 75 6718 4798 4.196 .238 .262 .214 .243 2.025 80 354 .235 .92 100 2440 9180 40 50 111 121 0 1959 538 1421 .262 1634 1096 3.818 .288 -1.933 -1.795
7 142 757 124 569 18 188 128 713 158 615 4 144 0 0 90 400 138 307 6 23 3 12 206 148 .096 10.444 36 3.206 3.342 4.642 80 385 5.078 .4 100 2620 9220 44 54 129 139 -50 832 625 207 11.477 784 158 .087 39.56 3.521 5.306
8 1236 1733 133 561 1103 1172 924 1434 170 623 791 873 0 0 980 1079 141 324 76 73 71 61 2275 1664 .941 1.063 1.104 1.171 1.066 2.15 52 289 1.151 .87 90 2750 9180 40 49 142 151 0 1904 616 1288 1.168 1576 959 .856 1.213 .224 .278
9 366 1154 118 493 248 661 383 1085 135 539 265 592 0 0 177 587 61 297 81 71 78 50 909 857 .375 2.665 2.234 2.653 2.565 2.086 32 206 4.253 .74 70 2910 9190 42 49 159 166 0 1268 542 726 2.929 1192 651 .341 2.455 1.55 1.296
10 218 715 125 452 93 263 149 601 148 493 24 149 0 0 191 475 99 240 27 42 15 21 356 173 .354 2.828 6.208 3.054 3.176 4.538 80 405 3.012 .77 100 3090 9220 44 54 176 186 -50 786 497 289 3.108 660 164 .322 6.822 1.636 2.77
11 224 694 141 518 83 176 177 611 173 559 36 93 0 0 182 399 119 266 25 28 13 20 259 129 .472 2.12 2.583 2.639 3.231 3.759 80 351 4.153 .51 100 3240 9220 44 54 191 201 -50 763 569 193 2.33 671 102 .429 2.839 1.22 1.505
12 218 683 140 495 78 188 145 583 159 550 5 88 0 0 203 365 96 280 25 32 20 11 266 93 .415 2.41 17.6 2.35 2.163 4.145 80 361 3.252 .63 100 3400 9220 44 54 207 217 -50 751 544 207 2.649 641 97 .378 19.341 1.405 4.274
13 214 594 119 459 95 135 144 585 132 512 25 126 0 0 174 294 75 277 36 31 25 10 230 151 .704 1.421 5.04 2.625 2.615 4.575 80 349 4.57 .45 100 3560 9220 44 54 223 233 -50 653 504 148 1.562 643 138 .64 5.538 .643 2.469
14 1257 2778 116 493 1141 2285 1161 2655 129 519 1045 2162 0 0 888 1714 77 240 84 86 82 78 3426 3207 .499 2.003 2.069 2.279 2.079 2.37 52 289 2.08 .94 90 3690 9180 40 49 236 245 0 3053 542 2511 2.201 2918 2376 .454 2.274 1.138 1.185
15 249 766 113 479 136 287 174 665 118 503 61 186 0 0 202 456 46 225 58 43 37 27 423 247 .474 2.11 3.049 3.035 2.974 2.875 80 406 4.168 .63 100 3870 9210 43 53 254 264 -50 842 526 315 2.319 731 204 .431 3.351 1.214 1.744
16 788 1836 105 510 683 1326 519 1331 115 547 414 821 0 0 689 1362 49 248 93 83 88 72 2009 1235 .515 1.941 1.983 1.91 1.915 2.189 80 397 2.116 .91 100 4000 9190 41 51 267 277 0 2018 560 1457 2.133 1463 902 .469 2.179 1.093 1.124
17 432 905 117 556 315 349 435 892 133 640 318 336 0 0 159 340 63 332 83 50 83 16 664 654 .903 1.108 1.057 1.157 1.118 1.895 12 80 4.169 .42 50 4160 9190 43 48 285 290 0 995 611 384 1.218 980 369 .821 1.161 .284 .215
18 167 521 107 466 60 55 124 445 117 485 17 -21 0 0 134 266 53 204 32 27 25 16 115 -4 1.091 .917 null 2.821 3.268 5.258 80 431 11.139 .2 100 4340 9210 43 53 301 311 -50 573 512 60 1.007 489 null .993 null .011 null
19 429 1108 120 476 309 632 470 1091 126 494 350 615 0 0 188 409 54 207 88 82 78 73 941 965 .489 2.045 1.757 1.879 1.857 2.492 52 244 2.787 .67 80 4490 9200 43 51 317 325 0 1218 523 695 2.248 1199 676 .445 1.931 1.168 .949
20 199 639 107 502 92 137 137 616 112 527 30 114 0 0 154 278 48 250 43 23 31 8 229 144 .672 1.489 3.8 1.879 2.493 5.201 80 382 9.548 .27 100 4650 9210 43 53 332 342 -50 702 552 151 1.636 677 125 .611 4.176 .711 2.062

Total number of rows: 37632

Table truncated, full table size 8467 Kbytes.




Supplementary data files not provided
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