NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM84141 Query DataSets for GSM84141
Status Public on Nov 19, 2005
Title 072801 Mock 02.00 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 02.00 hr.
Organism Homo sapiens
Characteristics 072801 Mock 02.00 hr.
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: T-cell, Costimulation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18938.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 3582 2940 234 689 3348 2251 2549 2122 242 731 2315 1433 0 0 2695 2054 75 311 98 85 96 76 5599 3748 1.487 .672 .619 .629 .663 2.156 80 442 .696 .91 110 1640 8680 32 43 64 75 0 4261 999 3262 .974 3075 2077 1.026 .897 -.037 -.157
2 1767 2001 232 683 1535 1318 1761 1908 232 697 1529 1225 0 0 685 661 72 261 100 98 100 92 2853 2754 1.165 .859 .801 .894 .894 1.901 52 248 .959 .81 90 1810 8680 33 42 82 91 0 2900 990 1910 1.244 2765 1775 .804 1.161 .315 .216
3 4077 6100 232 675 3845 5425 3763 6246 237 696 3531 5571 0 0 2278 2962 79 254 100 100 100 100 9270 9102 .709 1.411 1.578 1.465 1.452 1.445 52 252 1.383 .94 90 1970 8680 33 42 98 107 0 8841 978 7862 2.045 9052 8074 .489 2.287 1.032 1.193
4 4091 2727 233 644 3858 2083 4008 2569 241 685 3775 1925 0 0 2417 1201 72 254 98 96 98 94 5941 5700 1.852 .54 .51 .583 .502 1.712 52 239 .493 .9 90 2120 8670 32 41 113 122 0 3952 933 3019 .782 3723 2790 1.278 .739 -.354 -.436
5 3488 2143 254 641 3234 1502 3788 2104 311 714 3534 1463 0 0 2063 811 222 329 100 96 96 81 4736 4997 2.153 .464 .414 .525 .481 1.569 32 104 .415 .88 60 2270 8670 34 40 130 136 0 3106 929 2177 .673 3049 2120 1.486 .6 -.571 -.737
6 15383 3024 220 671 15163 2353 11533 2290 269 715 11313 1619 0 0 10252 1832 359 298 100 90 97 81 17516 12932 6.444 .155 .143 .137 .153 2.12 80 382 .155 .93 110 2430 8680 32 43 143 154 0 4383 972 3410 .225 3319 2346 4.446 .207 -2.153 -2.269
7 341 822 222 676 119 146 237 708 264 712 15 32 0 0 396 442 370 299 10 28 5 11 265 47 .815 1.227 2.133 2.291 2.156 2.85 80 331 .475 .27 100 2580 8730 38 48 159 169 -50 1191 980 212 1.778 1026 46 .562 3.092 .83 1.628
8 13512 4017 226 633 13286 3384 13126 3817 238 675 12900 3184 0 0 5781 1481 95 274 100 100 100 100 16670 16084 3.926 .255 .247 .258 .257 1.404 80 365 .242 .94 110 2740 8680 32 43 174 185 0 5822 917 4904 .369 5532 4614 2.709 .358 -1.438 -1.483
9 1973 2183 232 656 1741 1527 2157 2064 235 700 1925 1408 0 0 792 691 76 313 100 100 100 90 3268 3333 1.14 .877 .731 .904 .876 1.646 52 230 .87 .83 80 2890 8690 35 43 191 199 0 3164 951 2213 1.271 2991 2041 .787 1.06 .346 .084
10 3090 3674 231 721 2859 2953 2948 3566 247 750 2717 2845 0 0 1354 1172 98 317 100 100 100 100 5812 5562 .968 1.033 1.047 1.092 1.079 1.488 32 174 1.023 .93 70 3050 8690 35 42 207 214 0 5325 1045 4280 1.497 5168 4123 .668 1.518 .582 .602
11 2713 3604 234 738 2479 2866 2799 3488 264 775 2565 2750 0 0 983 1234 151 325 100 100 100 96 5345 5315 .865 1.156 1.072 1.131 1.202 1.564 32 160 1.096 .77 70 3200 8680 34 41 222 229 0 5223 1070 4154 1.676 5055 3986 .597 1.554 .745 .636
12 1581 3365 264 795 1317 2570 1296 2630 291 861 1032 1835 0 0 1118 2168 136 419 92 88 82 73 3887 2867 .512 1.951 1.778 2.02 1.888 1.901 52 227 2.995 .74 80 3370 8680 34 42 239 247 0 4877 1152 3725 2.828 3812 2659 .354 2.577 1.5 1.366
13 2236 4063 399 979 1837 3084 2354 4179 690 1622 1955 3200 0 0 1210 1760 1251 1737 65 71 34 46 4921 5155 .596 1.679 1.637 1.853 1.642 1.696 32 121 1.702 .89 60 3520 8690 36 42 255 261 0 5888 1419 4470 2.433 6057 4638 .411 2.372 1.283 1.246
14 2280 4471 287 884 1993 3587 1154 2233 782 1636 867 1349 0 0 3549 6019 1585 2231 32 40 15 21 5580 2216 .556 1.8 1.556 2.834 2.413 2.87 80 413 1.615 .95 100 3670 8740 39 49 268 278 -50 6480 1281 5199 2.608 3236 1955 .383 2.255 1.383 1.173
15 1686 2660 258 779 1428 1881 1352 2494 406 967 1094 1715 0 0 1136 1475 632 925 63 65 42 48 3309 2809 .759 1.317 1.568 1.333 1.366 2.135 52 206 1.408 .88 80 3820 8680 34 42 284 292 0 3855 1129 2726 1.909 3614 2486 .524 2.272 .933 1.184
16 5004 4363 235 709 4769 3654 3322 3258 252 756 3087 2549 0 0 3989 3013 103 328 100 98 100 92 8423 5636 1.305 .766 .826 .781 .794 1.529 80 469 .751 .96 110 3990 8690 33 44 299 310 0 6323 1028 5296 1.11 4722 3694 .901 1.197 .151 .259
17 2556 2534 281 805 2275 1729 2529 2547 329 842 2248 1742 0 0 541 593 154 303 100 100 100 100 4004 3990 1.316 .76 .775 .735 .799 1.368 12 52 .858 .89 50 4150 8680 35 40 318 323 0 3672 1167 2506 1.101 3691 2525 .908 1.123 .139 .167
18 1439 1883 231 710 1208 1173 1390 1831 245 707 1159 1121 0 0 707 736 84 279 100 90 93 78 2381 2280 1.03 .971 .967 1.032 1.026 2.029 32 134 1.083 .78 60 4300 8710 38 44 333 339 0 2729 1029 1700 1.407 2654 1625 .711 1.402 .493 .487
19 2789 5162 231 674 2558 4488 2688 5433 245 694 2457 4759 0 0 1158 1608 87 274 100 100 100 100 7046 7216 .57 1.754 1.937 1.828 1.896 1.469 80 397 1.757 .93 100 4460 8690 34 44 347 357 0 7481 977 6504 2.543 7874 6897 .393 2.807 1.346 1.489
20 1338 1764 267 770 1071 994 1285 1630 303 782 1018 860 0 0 330 542 154 284 100 91 100 83 2065 1878 1.077 .928 .845 .828 .954 2.411 12 52 1.401 .7 50 4630 8680 35 40 366 371 0 2557 1116 1441 1.345 2362 1246 .743 1.224 .428 .292

Total number of rows: 37632

Table truncated, full table size 8785 Kbytes.




Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap