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Sample GSM84130 Query DataSets for GSM84130
Status Public on Nov 19, 2005
Title 072801 B7-2 01.00 hr. T-Cell
Sample type RNA
 
Channel 1
Source name 10 amplified MOATS pool
Organism Homo sapiens
Characteristics 10 amplified MOATS pool
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 072801 B7-2 01.00 hr.
Organism Homo sapiens
Characteristics 072801 B7-2 01.00 hr.
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: T-cell, Costimulation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18899.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 Nov 17, 2005
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)
GSE3630 T-cell co-stimulation

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 3264 1679 161 377 3103 1302 2930 1544 226 401 2769 1167 0 0 2235 1015 308 175 96 90 82 76 4405 3936 2.383 .42 .421 .407 .412 1.984 52 268 .412 .91 90 1790 8530 36 45 68 77 0 2181 490 1691 .545 2005 1516 1.835 .547 -.876 -.869
2 1007 1120 167 392 840 728 1037 1084 183 403 870 692 0 0 421 350 124 163 96 98 92 84 1568 1562 1.154 .867 .795 .908 .856 1.904 52 252 .969 .77 90 1950 8530 36 45 84 93 0 1455 509 945 1.126 1408 899 .888 1.033 .171 .047
3 2840 3303 172 391 2668 2912 2819 3137 203 425 2647 2746 0 0 1972 1803 274 276 92 96 82 88 5580 5393 .916 1.091 1.037 1.2 1.081 1.696 52 248 1.021 .96 90 2110 8530 36 45 100 109 0 4290 508 3782 1.417 4074 3566 .705 1.347 .503 .43
4 3005 1679 166 362 2839 1317 3159 1765 195 404 2993 1403 0 0 2078 854 266 268 88 84 84 78 4156 4396 2.156 .464 .469 .547 .488 2.334 52 270 .42 .91 90 2270 8530 36 45 116 125 0 2181 470 1710 .602 2292 1822 1.66 .609 -.731 -.716
5 3667 2009 324 444 3343 1565 3734 2035 375 479 3410 1591 0 0 1207 524 192 203 100 100 100 100 4908 5001 2.136 .468 .467 .479 .476 1.35 12 46 .441 .88 50 2420 8520 37 42 133 138 0 2609 577 2032 .608 2643 2066 1.645 .606 -.718 -.723
6 2223 513 183 391 2040 122 221 419 1175 486 38 28 0 0 4468 384 3647 386 16 12 7 6 2162 66 16.721 .06 .737 .437 .55 7.344 80 381 .08 .89 100 2570 8590 42 52 146 156 -50 666 508 158 .078 544 36 12.875 .957 -3.687 -.064
7 213 430 169 423 44 7 183 380 581 466 14 -43 0 0 126 311 2159 287 0 8 0 1 51 -29 6.286 .159 null 2.637 3.44 3.804 80 316 1.895 .37 100 2720 8590 42 52 161 171 -50 558 549 9 .207 494 null 4.84 null -2.275 null
8 1269 499 167 397 1102 102 203 432 567 450 36 35 0 0 2312 345 1375 282 20 16 15 6 1204 71 10.804 .093 .972 .527 .387 6.563 80 367 .151 .88 100 2880 8590 42 52 177 187 -50 648 516 132 .12 561 45 8.319 1.263 -3.056 .336
9 1146 1147 162 364 984 783 1185 1120 310 403 1023 756 0 0 458 429 716 229 67 90 17 73 1767 1779 1.257 .796 .739 .803 .782 2.326 52 296 .616 .63 90 3030 8550 38 47 192 201 0 1490 473 1017 1.033 1455 982 .968 .96 .047 -.059
10 2474 3062 175 364 2299 2698 2691 3424 191 404 2516 3060 0 0 1138 1249 83 184 100 96 100 96 4997 5576 .852 1.174 1.216 1.186 1.19 1.788 32 148 1.162 .95 70 3210 8540 38 45 211 218 0 3977 473 3504 1.524 4447 3974 .656 1.58 .608 .659
11 1341 1402 162 373 1179 1029 1226 1460 172 398 1064 1087 0 0 955 781 73 172 90 82 78 69 2208 2151 1.146 .873 1.022 .938 .875 2.202 52 196 .855 .9 80 3350 8540 38 46 225 233 0 1821 484 1336 1.133 1896 1412 .882 1.327 .181 .408
12 1746 2232 161 398 1585 1834 1318 1815 174 400 1157 1417 0 0 1396 1489 66 164 90 92 84 84 3419 2574 .864 1.157 1.225 1.277 1.198 2.404 52 204 1.135 .95 80 3510 8540 38 46 241 249 0 2899 517 2382 1.503 2357 1840 .665 1.591 .588 .67
13 1077 958 164 390 913 568 1221 855 177 408 1057 465 0 0 644 445 60 192 93 78 84 65 1481 1522 1.607 .622 .44 .596 .612 2.758 32 116 .592 .66 60 3660 8560 41 47 257 263 0 1244 506 738 .808 1110 604 1.238 .571 -.308 -.808
14 2616 3226 163 344 2453 2882 1343 1770 175 365 1180 1426 0 0 2669 2925 66 155 96 97 94 95 5335 2606 .851 1.175 1.208 1.366 1.226 1.97 120 556 1.132 .96 120 3820 8560 38 50 270 282 0 4190 447 3743 1.526 2299 1852 .655 1.569 .61 .65
15 3147 1740 184 381 2963 1359 1835 1817 240 434 1651 1436 0 0 5643 755 153 239 93 90 87 84 4322 3087 2.18 .459 .87 .801 .895 2.516 32 87 .113 .5 60 3970 8530 38 44 288 294 0 2260 495 1765 .596 2360 1865 1.679 1.13 -.747 .176
16 1365 1163 174 404 1191 759 212 576 300 503 38 172 0 0 2037 1216 406 387 36 38 36 32 1950 210 1.569 .637 4.526 1.333 .76 4.011 80 467 .673 .95 100 4130 8600 43 53 302 312 -50 1510 525 986 .828 748 223 1.208 5.878 -.273 2.555
17 1058 1475 170 340 888 1135 1152 1533 182 388 982 1193 0 0 588 592 70 173 90 93 81 90 2023 2175 .782 1.278 1.215 1.705 1.392 2.196 32 122 1.167 .86 60 4300 8560 41 47 321 327 0 1916 442 1474 1.66 1991 1549 .602 1.578 .731 .658
18 1218 1849 188 437 1030 1412 1344 1754 200 463 1156 1317 0 0 435 334 64 205 100 100 100 100 2442 2473 .729 1.371 1.139 1.522 1.376 1.699 12 58 1.245 .85 50 4450 8540 39 44 336 341 0 2401 568 1834 1.78 2278 1710 .562 1.48 .832 .565
19 1407 5057 168 369 1239 4688 1520 5346 178 387 1352 4977 0 0 715 2107 103 188 98 100 95 100 5927 6329 .264 3.784 3.681 4.283 3.847 1.674 80 463 3.713 .94 110 4600 8550 37 48 348 359 0 6568 479 6088 4.914 6943 6464 .204 4.781 2.297 2.257
20 733 1243 162 428 571 815 789 1217 178 434 627 789 0 0 223 366 68 156 91 91 91 91 1386 1416 .701 1.427 1.258 1.316 1.279 1.606 12 64 1.597 .78 50 4750 8550 40 45 366 371 0 1614 556 1058 1.854 1581 1025 .539 1.634 .89 .709

Total number of rows: 37632

Table truncated, full table size 8695 Kbytes.




Supplementary data files not provided
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