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Sample GSM84184 Query DataSets for GSM84184
Status Public on Nov 19, 2005
Title 072801 B7-2 06.00 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 06.00 hr.
Organism Homo sapiens
Characteristics 072801 B7-2 06.00 hr.
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: T-cell, Costimulation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18958.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 3675 1999 164 291 3511 1708 2198 1173 175 306 2034 882 0 0 3166 1851 68 145 98 90 98 83 5219 2916 2.056 .486 .434 .395 .447 2.093 80 490 .479 .86 110 1610 8370 41 52 50 61 0 2738 399 2340 .666 1607 1208 1.501 .594 -.586 -.751
2 770 884 157 273 613 611 710 882 163 279 553 609 0 0 421 355 55 107 92 94 90 88 1224 1162 1.003 .997 1.101 1.013 1.033 2.61 52 278 .977 .79 90 1770 8380 43 52 67 76 0 1211 374 837 1.365 1208 834 .732 1.509 .449 .593
3 2472 3147 158 280 2314 2867 1690 2016 174 319 1532 1736 0 0 2229 2663 96 288 96 91 90 83 5181 3268 .807 1.239 1.133 1.379 1.199 2.093 80 325 1.222 .96 100 1920 8360 41 51 82 92 0 4311 384 3927 1.697 2762 2378 .589 1.552 .763 .634
4 2631 1531 162 296 2469 1235 2104 1386 208 346 1942 1090 0 0 1708 740 237 305 96 94 96 73 3704 3032 1.999 .5 .561 .529 .489 1.68 52 288 .454 .85 90 2080 8350 40 49 98 107 0 2097 405 1692 .685 1899 1493 1.459 .769 -.545 -.379
5 1992 1235 177 297 1815 938 2091 1161 213 317 1914 864 0 0 1374 722 117 144 90 78 84 71 2753 2778 1.935 .517 .451 .52 .491 1.759 32 109 .498 .9 60 2260 8360 43 49 118 124 0 1692 407 1285 .708 1590 1184 1.413 .618 -.498 -.693
6 2529 546 176 297 2353 249 254 376 1049 367 78 79 0 0 5334 551 3606 312 17 23 10 11 2602 157 9.45 .106 1.013 .473 .331 5.96 80 379 .078 .92 100 2400 8410 46 56 130 140 -50 748 407 341 .145 515 108 6.898 1.387 -2.786 .472
7 239 325 178 310 61 15 190 305 333 344 12 -5 0 0 220 140 986 204 1 8 0 1 76 7 4.067 .246 null 1.958 2.028 4.004 80 354 .499 .47 100 2560 8410 46 56 146 156 -50 445 425 21 .337 418 null 2.969 null -1.57 null
8 11072 2616 166 300 10906 2316 8845 2176 175 317 8679 1876 0 0 6801 1458 74 139 100 98 100 96 13222 10555 4.709 .212 .216 .223 .218 1.539 80 440 .205 .96 110 2720 8360 40 51 161 172 0 3584 411 3173 .291 2981 2570 3.438 .296 -1.781 -1.756
9 1319 1458 171 303 1148 1155 1355 1394 203 336 1184 1091 0 0 461 462 125 179 100 96 100 96 2303 2275 .994 1.006 .921 1.006 1.009 1.579 32 148 .978 .87 70 2870 8350 41 48 178 185 0 1997 415 1582 1.378 1910 1495 .726 1.262 .463 .336
10 3356 3031 169 277 3187 2754 3230 2781 190 312 3061 2504 0 0 1510 1590 90 145 100 100 100 100 5941 5565 1.157 .864 .818 .887 .87 1.581 32 134 .898 .9 60 3030 8380 45 51 195 201 0 4152 379 3773 1.184 3810 3430 .845 1.121 .243 .164
11 1803 1770 175 323 1628 1447 1932 1716 205 341 1757 1393 0 0 863 758 110 148 93 96 90 93 3075 3150 1.125 .889 .793 .894 .913 1.45 32 114 .899 .93 60 3180 8360 43 49 210 216 0 2425 442 1982 1.218 2351 1908 .821 1.086 .284 .119
12 1673 1921 173 334 1500 1587 1633 2036 202 350 1460 1702 0 0 803 849 114 159 93 93 90 90 3087 3162 .945 1.058 1.166 1.108 1.062 1.569 32 114 1.099 .94 60 3340 8360 43 49 226 232 0 2632 458 2174 1.449 2789 2332 .69 1.597 .535 .675
13 1610 1699 188 317 1422 1382 1705 1696 207 329 1517 1379 0 0 855 696 90 147 96 96 93 93 2804 2896 1.029 .972 .909 1.151 1.039 1.801 32 94 .916 .92 60 3520 8360 43 49 244 250 0 2327 434 1893 1.331 2323 1889 .751 1.245 .413 .316
14 3291 3052 171 312 3120 2740 1640 1622 183 330 1469 1310 0 0 3769 3106 87 173 96 99 94 94 5860 2779 1.139 .878 .892 .987 .875 1.905 120 540 .838 .96 120 3660 8370 41 53 255 267 0 4181 427 3753 1.203 2222 1795 .831 1.222 .267 .289
15 1866 1544 189 352 1677 1192 1734 1561 228 380 1545 1209 0 0 958 637 133 166 96 100 96 90 2869 2754 1.407 .711 .783 .711 .694 1.716 32 102 .688 .87 60 3810 8360 43 49 273 279 0 2115 482 1633 .974 2138 1656 1.027 1.072 -.038 .1
16 3796 3152 170 307 3626 2845 2488 1937 185 321 2318 1630 0 0 3394 2687 85 135 97 98 97 96 6471 3948 1.275 .785 .703 .794 .763 2.148 80 489 .782 .96 110 3980 8370 41 52 287 298 0 4318 421 3897 1.075 2653 2233 .93 .963 .104 -.054
17 1856 1650 227 362 1629 1288 1856 1767 250 408 1629 1405 0 0 569 474 147 224 100 100 100 100 2917 3034 1.265 .791 .862 .786 .737 1.306 12 64 .798 .88 50 4120 8360 43 48 304 309 0 2260 496 1764 1.083 2421 1925 .923 1.181 .115 .241
18 1175 1390 183 335 992 1055 1179 1344 190 343 996 1009 0 0 673 703 75 136 90 93 90 87 2047 2005 .94 1.064 1.013 1.076 1.048 1.954 32 102 1.088 .91 60 4300 8360 43 49 322 328 0 1904 459 1445 1.457 1841 1382 .686 1.388 .543 .473
19 2081 5843 170 306 1911 5537 2252 6474 175 317 2082 6168 0 0 1272 3512 54 123 100 100 100 100 7448 8250 .345 2.897 2.963 2.972 2.787 1.534 80 456 3.006 .96 110 4440 8370 41 52 333 344 0 8004 419 7585 3.969 8868 8449 .252 4.058 1.989 2.021
20 907 1414 166 346 741 1068 867 1452 179 384 701 1106 0 0 349 335 80 176 100 100 100 100 1809 1807 .694 1.441 1.578 1.527 1.77 1.468 12 64 1.46 .8 50 4600 8360 43 48 352 357 0 1937 474 1463 1.974 1989 1515 .506 2.161 .981 1.112

Total number of rows: 37632

Table truncated, full table size 8698 Kbytes.




Supplementary data files not provided
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