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Sample GSM91839 Query DataSets for GSM91839
Status Public on Jan 11, 2006
Title "282 Day0 in-vivo SP Inf, PBMC 3rd TC, 2nd amp"
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 "282 Day0 in-vivo SP Inf, PBMC 3rd TC, 2nd amp"
Organism Homo sapiens
Characteristics "282 Day0 in-vivo SP Inf, PBMC 3rd TC, 2nd amp"
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/21490.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 1470 674 99 265 1371 409 1665 636 143 288 1566 371 0 0 654 227 153 142 96 90 96 62 1780 1937 3.352 .298 .237 .305 .322 1.865 32 214 .28 .8 70 1900 9450 47 54 52 59 0 853 335 518 .378 805 470 2.648 .3 -1.405 -1.738
2 142 311 97 259 45 52 112 271 133 293 15 12 0 0 103 161 165 160 12 26 2 8 97 27 .865 1.156 .8 1.659 1.736 3.739 80 401 1.056 .6 100 2070 9460 47 57 68 78 -50 394 328 66 1.463 343 15 .684 1.013 .549 .018
3 1482 1312 102 274 1380 1038 1548 1363 185 324 1446 1089 0 0 643 560 265 189 100 100 93 87 2418 2535 1.329 .752 .753 .708 .664 1.664 32 150 .752 .86 70 2200 9430 45 52 82 89 0 1661 347 1314 .952 1725 1378 1.05 .953 -.071 -.069
4 1890 657 101 287 1789 370 1751 664 120 306 1650 377 0 0 988 286 111 156 100 73 100 57 2159 2027 4.835 .207 .228 .192 .232 1.879 80 446 .224 .82 100 2330 9440 45 55 94 104 0 832 363 468 .262 841 477 3.82 .289 -1.933 -1.79
5 247 372 104 290 143 82 163 353 119 303 59 63 0 0 225 178 67 133 47 31 32 15 225 122 1.744 .573 1.068 1.064 .853 4.288 80 369 .807 .47 100 2540 9460 47 57 115 125 -50 471 367 104 .726 447 80 1.378 1.352 -.462 .435
6 4101 1346 96 297 4005 1049 3430 1117 106 311 3334 820 0 0 2580 790 50 135 100 90 100 85 5054 4154 3.818 .262 .246 .245 .253 1.778 80 377 .278 .9 100 2650 9430 44 54 126 136 0 1704 376 1328 .332 1414 1038 3.016 .311 -1.593 -1.683
7 123 330 105 280 18 50 103 302 136 303 -2 22 0 0 69 141 187 149 1 21 0 8 68 20 .36 2.778 null 2.184 2.239 4.41 80 371 .28 .28 100 2850 9460 47 57 146 156 -50 418 354 63 3.516 382 28 .284 null 1.814 null
8 1277 1010 96 277 1181 733 852 768 120 294 756 491 0 0 1220 777 158 150 90 71 73 62 1914 1247 1.611 .621 .649 .542 .631 2.139 80 399 .604 .91 100 2980 9440 45 55 159 169 0 1278 351 928 .786 972 622 1.273 .822 -.348 -.283
9 312 914 104 313 208 601 338 857 136 340 234 544 0 0 126 384 87 164 83 83 58 83 809 778 .346 2.889 2.325 2.255 1.79 1.89 12 90 3.723 .66 50 3160 9440 47 52 179 184 0 1157 396 761 3.657 1085 689 .273 2.943 1.871 1.557
10 242 458 98 283 144 175 146 343 114 297 48 60 0 0 238 363 70 137 40 35 28 23 319 108 .823 1.215 1.25 1.546 1.372 3.508 80 403 1.911 .73 100 3320 9460 47 57 193 203 -50 580 358 222 1.538 434 76 .65 1.582 .621 .662
11 213 366 104 282 109 84 149 313 120 288 45 31 0 0 186 202 70 130 41 32 30 17 193 76 1.298 .771 .689 1.609 1.487 3.887 80 355 1.622 .56 100 3470 9460 47 57 208 218 -50 463 357 106 .975 396 39 1.025 .872 -.036 -.198
12 479 763 120 259 359 504 476 643 127 271 356 384 0 0 116 385 64 93 100 100 91 75 863 740 .712 1.404 1.079 1.161 1.226 2.461 12 72 2.45 .54 50 3610 9420 45 50 224 229 0 966 328 638 1.777 814 486 .563 1.365 .83 .449
13 183 391 102 282 81 109 160 374 114 299 58 92 0 0 113 182 54 121 52 42 33 23 190 150 .743 1.346 1.586 1.896 1.789 3.076 80 382 3.415 .41 100 3790 9460 47 57 240 250 -50 495 357 138 1.703 473 116 .587 2.008 .768 1.006
14 1112 1413 104 303 1008 1110 710 1254 115 343 606 951 0 0 937 890 57 201 95 87 91 66 2118 1557 .908 1.101 1.569 1.344 1.165 2.058 80 417 1.108 .91 110 3910 9440 44 55 251 262 0 1789 384 1405 1.394 1587 1204 .717 1.986 .479 .99
15 206 501 98 300 108 201 140 461 111 329 42 161 0 0 173 261 54 198 40 45 30 21 309 203 .537 1.861 3.833 2.711 2.235 3.914 80 366 3.003 .52 100 4100 9460 47 57 271 281 -50 634 380 254 2.356 584 204 .424 4.852 1.236 2.279
16 1032 1887 97 278 935 1609 835 1577 105 298 738 1299 0 0 650 1199 47 140 100 98 97 97 2544 2037 .581 1.721 1.76 1.691 1.679 1.874 80 420 1.823 .92 110 4220 9440 44 55 282 293 0 2389 352 2037 2.178 1996 1644 .459 2.228 1.123 1.156
17 131 298 92 258 39 40 103 270 97 282 11 12 0 0 88 132 48 141 35 21 22 3 79 23 .975 1.026 1.091 1.51 1.344 3.54 80 400 3.779 .36 100 4410 9450 46 56 302 312 -50 377 327 51 1.298 342 15 .77 1.381 .377 .466
18 161 327 88 270 73 57 120 304 106 297 32 34 0 0 108 148 82 172 31 12 22 3 130 66 1.281 .781 1.063 1.16 1.365 4.772 80 365 3.482 .35 100 4560 9450 46 56 317 327 -50 414 342 72 .988 385 43 1.012 1.345 -.017 .428
19 63 229 79 255 -16 -26 51 218 97 287 -28 -37 0 0 71 112 80 172 3 7 2 0 -42 -65 null null null 2.122 3.279 4.471 80 418 2.038 .79 100 4720 9450 46 56 333 343 -50 290 323 -33 null 276 null null null null null
20 98 266 85 244 13 22 66 228 89 257 -19 -16 0 0 118 146 42 118 16 21 8 8 35 -35 .591 1.692 null 2.114 2.137 3.823 80 317 2.373 .46 100 4880 9450 46 56 349 359 -50 337 309 28 2.142 289 null .467 null 1.099 null

Total number of rows: 37632

Table truncated, full table size 8369 Kbytes.




Supplementary data files not provided
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