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Sample GSM84127 Query DataSets for GSM84127
Status Public on Nov 19, 2005
Title 072801 Mock 12.00 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 Mock 12.00 hr.
Organism Homo sapiens
Characteristics 072801 Mock 12.00 hr.
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: T-cell, Costimulation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18896.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 5564 3145 190 250 5374 2895 6163 3192 195 260 5973 2942 0 0 2060 1148 54 93 98 100 98 100 8269 8915 1.856 .539 .493 .54 .544 1.366 80 460 .53 .97 110 1660 8470 27 38 54 65 0 3145 250 2895 .539 3192 2942 1.856 .493 -.892 -1.022
2 1157 1538 203 286 954 1252 1082 1577 596 1585 879 1291 0 0 582 535 2799 7197 0 0 0 0 2206 2170 .762 1.312 1.469 1.441 1.435 1.559 80 302 1.219 .91 100 1820 8470 28 38 71 81 0 1538 286 1252 1.312 1577 1291 .762 1.469 .392 .555
3 1042 1204 242 361 800 843 316 487 1198 2388 74 126 0 0 1657 1917 3463 7531 7 3 1 0 1643 200 .949 1.054 1.703 1.824 1.601 2.529 80 311 1.311 .98 100 1970 8510 32 42 86 96 -50 1204 361 843 1.054 487 126 .949 1.703 .076 .768
4 3987 3416 237 343 3750 3073 3222 2970 721 945 2985 2627 0 0 3153 2485 1797 2427 67 52 40 14 6823 5612 1.22 .819 .88 .85 .814 1.424 120 453 .807 .97 120 2140 8480 28 40 102 114 0 3416 343 3073 .819 2970 2627 1.22 .88 -.287 -.184
5 1893 1574 510 584 1383 990 1691 1549 630 650 1181 965 0 0 752 486 495 420 93 88 67 58 2373 2146 1.397 .716 .817 .727 .714 1.577 80 339 .637 .89 100 2280 8510 32 42 117 127 -50 1574 584 990 .716 1549 965 1.397 .817 -.482 -.291
6 17817 2631 234 304 17583 2327 20186 2800 523 443 19952 2496 0 0 10266 1381 1001 325 100 92 94 90 19910 22448 7.556 .132 .125 .128 .135 1.541 52 282 .128 .96 90 2440 8450 26 35 133 142 0 2631 304 2327 .132 2800 2496 7.556 .125 -2.918 -2.999
7 235 328 188 257 47 71 179 287 310 304 -9 30 0 0 171 181 829 170 0 23 0 10 118 21 .662 1.511 null 1.461 1.604 3.915 80 373 .988 .5 100 2600 8510 32 42 149 159 -50 328 257 71 1.511 287 30 .662 null .595 null
8 6506 1882 170 238 6336 1644 4145 1345 176 254 3975 1107 0 0 5873 1304 57 90 100 97 100 96 7980 5082 3.854 .259 .278 .352 .285 2.002 80 391 .226 .95 110 2750 8460 26 37 163 174 0 1882 238 1644 .259 1345 1107 3.854 .278 -1.946 -1.844
9 1076 1248 162 243 914 1005 920 1066 164 244 758 823 0 0 531 552 46 87 96 100 95 100 1919 1581 .909 1.1 1.086 1.141 1.14 1.633 80 293 1.09 .93 100 2910 8470 28 38 180 190 0 1248 243 1005 1.1 1066 823 .909 1.086 .137 .119
10 1063 1360 160 244 903 1116 602 1011 164 248 442 767 0 0 848 870 46 94 98 97 90 95 2019 1209 .809 1.236 1.735 1.552 1.276 1.891 80 318 1.133 .96 100 3060 8470 28 38 195 205 0 1360 244 1116 1.236 1011 767 .809 1.735 .306 .795
11 1183 1278 176 247 1007 1031 567 869 179 254 391 622 0 0 1082 856 48 93 93 95 87 93 2038 1013 .977 1.024 1.591 1.438 1.319 2.977 80 334 .889 .92 100 3220 8470 28 38 211 221 0 1278 247 1031 1.024 869 622 .977 1.591 .034 .67
12 1123 1681 168 230 955 1451 529 996 177 242 361 766 0 0 1093 1406 53 95 92 98 83 95 2406 1127 .658 1.519 2.122 2.09 1.589 2.287 80 335 1.397 .96 100 3390 8470 28 38 228 238 0 1681 230 1451 1.519 996 766 .658 2.122 .603 1.085
13 678 1067 164 232 514 835 461 892 170 244 297 660 0 0 519 623 55 94 82 94 73 88 1349 957 .616 1.625 2.222 2.204 1.697 2.437 52 252 1.463 .9 90 3550 8460 27 36 244 253 0 1067 232 835 1.625 892 660 .616 2.222 .7 1.152
14 2752 3704 165 233 2587 3471 1516 2224 172 244 1351 1991 0 0 2654 3383 64 94 92 98 89 96 6058 3342 .745 1.342 1.474 1.6 1.433 2.272 120 465 1.314 .96 120 3700 8470 27 39 258 270 0 3704 233 3471 1.342 2224 1991 .745 1.474 .424 .559
15 738 1005 161 231 577 774 471 825 165 243 310 594 0 0 625 563 48 84 88 95 78 93 1351 904 .745 1.341 1.916 1.886 1.446 2.417 80 296 1.096 .91 100 3850 8470 28 38 274 284 0 1005 231 774 1.341 825 594 .745 1.916 .424 .938
16 3640 2917 160 229 3480 2688 1852 1735 161 241 1692 1506 0 0 3374 2223 45 118 100 100 100 100 6168 3198 1.295 .772 .89 .912 .844 1.663 80 440 .7 .96 110 4010 8470 27 38 289 300 0 2917 229 2688 .772 1735 1506 1.295 .89 -.373 -.168
17 534 1250 158 237 376 1013 344 1011 158 240 186 774 0 0 381 708 43 86 76 100 63 98 1389 960 .371 2.694 4.161 3.541 2.569 2.362 52 298 2.405 .91 90 4170 8470 28 37 306 315 0 1250 237 1013 2.694 1011 774 .371 4.161 1.43 2.057
18 503 1107 151 238 352 869 353 825 161 242 202 587 0 0 354 770 58 83 73 94 61 84 1221 789 .405 2.469 2.906 3.121 2.419 2.642 52 262 2.493 .86 90 4330 8460 27 36 322 331 0 1107 238 869 2.469 825 587 .405 2.906 1.304 1.539
19 896 2632 154 226 742 2406 772 2150 165 236 618 1924 0 0 577 1617 71 92 90 99 83 95 3148 2542 .308 3.243 3.113 3.503 3.539 2.322 120 494 3.241 .92 120 4480 8470 27 39 336 348 0 2632 226 2406 3.243 2150 1924 .308 3.113 1.697 1.638
20 431 1318 153 230 278 1088 412 868 165 237 259 638 0 0 263 839 82 100 63 100 51 84 1366 897 .256 3.914 2.463 4.229 3.815 2.147 52 285 3.781 .9 90 4650 8470 28 37 354 363 0 1318 230 1088 3.914 868 638 .256 2.463 1.969 1.301

Total number of rows: 37632

Table truncated, full table size 8677 Kbytes.




Supplementary data files not provided
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