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Sample GSM84138 Query DataSets for GSM84138
Status Public on Nov 19, 2005
Title 072801 Mock 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 Mock 06.00 hr.
Organism Homo sapiens
Characteristics 072801 Mock 06.00 hr.
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: T-cell, Costimulation
Image: http://smd.stanford.edu/MicroArray/gifs/2001-08/18935.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 2593 1988 200 399 2393 1589 1923 1428 208 423 1723 1029 0 0 1874 1204 69 167 98 98 97 97 3982 2752 1.506 .664 .597 .71 .636 2.049 80 456 .633 .9 110 1770 8860 42 53 62 73 0 1949 391 1558 .651 1400 1009 1.536 .586 -.619 -.772
2 1312 1812 282 587 1030 1225 1320 1787 293 590 1038 1200 0 0 219 444 98 188 100 100 100 91 2255 2238 .841 1.189 1.156 1.119 1.146 1.468 12 46 1.348 .9 50 1940 8840 43 48 82 87 0 1776 575 1201 1.166 1752 1176 .858 1.133 .222 .181
3 2125 3630 200 399 1925 3231 1615 2851 213 414 1415 2452 0 0 1584 2160 76 155 96 95 96 95 5156 3867 .596 1.678 1.733 1.74 1.716 1.87 80 284 1.578 .93 100 2090 8860 43 53 95 105 0 3559 391 3168 1.646 2795 2404 .608 1.699 .719 .765
4 2933 2207 197 401 2736 1806 2813 2017 209 432 2616 1616 0 0 1470 959 71 173 100 98 98 98 4542 4232 1.515 .66 .618 .701 .657 1.623 52 266 .629 .91 90 2240 8860 43 52 110 119 0 2164 393 1771 .647 1977 1584 1.545 .606 -.628 -.724
5 1898 1764 208 424 1690 1340 1787 1656 227 434 1579 1232 0 0 1114 602 103 167 100 100 100 100 3030 2811 1.261 .793 .78 .942 .847 1.813 32 92 .687 .87 60 2410 8850 44 50 129 135 0 1729 416 1314 .777 1624 1208 1.286 .765 -.363 -.387
6 8734 1576 196 404 8538 1172 5907 1214 215 421 5711 810 0 0 7312 968 148 162 100 90 98 78 9710 6521 7.285 .137 .142 .152 .139 2.042 80 292 .124 .91 100 2560 8850 42 52 142 152 0 1545 396 1149 .135 1190 794 7.431 .139 -2.893 -2.846
7 367 587 204 390 163 197 255 563 223 406 51 173 0 0 300 263 115 152 35 52 26 28 360 224 .827 1.209 3.392 1.59 1.332 3.551 80 264 .313 .28 100 2720 8870 44 54 158 168 -50 575 382 193 1.185 552 170 .844 3.326 .245 1.734
8 7741 3168 203 411 7538 2757 6845 3000 224 439 6642 2589 0 0 3885 1310 110 191 100 100 100 100 10295 9231 2.734 .366 .39 .373 .366 1.481 80 281 .339 .94 110 2870 8850 41 52 172 183 0 3106 403 2703 .359 2941 2538 2.789 .382 -1.48 -1.388
9 1181 1589 219 437 962 1152 1054 1599 246 485 835 1162 0 0 354 505 122 225 100 100 100 87 2114 1997 .835 1.198 1.392 1.146 1.093 1.604 32 144 1.335 .81 70 3030 8850 43 50 190 197 0 1558 428 1129 1.174 1568 1139 .852 1.364 .231 .448
10 1310 1944 195 426 1115 1518 1135 1761 204 446 940 1335 0 0 933 1121 71 168 96 88 94 80 2633 2275 .735 1.361 1.42 1.463 1.411 1.911 52 207 1.303 .93 80 3200 8860 44 52 207 215 0 1906 418 1488 1.335 1726 1309 .749 1.392 .417 .478
11 1018 1672 191 394 827 1278 875 1605 199 413 684 1211 0 0 694 915 59 156 88 90 80 80 2105 1895 .647 1.545 1.77 1.713 1.456 2.376 52 174 1.518 .86 80 3360 8850 43 51 223 231 0 1639 386 1253 1.515 1574 1187 .66 1.736 .599 .796
12 680 1516 209 457 471 1059 392 955 239 515 183 498 0 0 678 1270 147 316 57 65 37 43 1530 681 .445 2.248 2.721 2.53 2.292 2.167 80 386 2.213 .87 110 3520 8850 41 52 237 248 0 1486 448 1038 2.204 936 488 .454 2.668 1.14 1.416
13 1441 2099 290 580 1151 1519 1419 2118 303 585 1129 1538 0 0 764 778 140 207 83 91 83 91 2670 2667 .758 1.32 1.362 1.299 1.388 1.376 12 52 1.353 .89 50 3680 8850 44 49 256 261 0 2058 569 1489 1.294 2076 1508 .773 1.336 .372 .417
14 3112 5993 191 438 2921 5555 1791 2745 350 807 1600 2307 0 0 3249 5679 1085 2404 63 50 36 40 8476 3907 .526 1.902 1.442 2.191 2.1 2.217 52 305 1.935 .94 90 3840 8880 45 54 270 279 0 5875 429 5446 1.864 2691 2262 .536 1.414 .899 .499
15 817 2319 197 414 620 1905 454 1397 339 452 257 983 0 0 945 2200 1265 230 13 84 5 71 2525 1240 .325 3.073 3.825 3.417 3.201 2.186 52 204 1.655 .42 90 3970 8840 41 50 283 292 0 2274 406 1868 3.012 1370 964 .332 3.75 1.591 1.907
16 2022 3616 188 429 1834 3187 652 1579 272 482 464 1150 0 0 5062 7051 881 281 38 60 22 56 5021 1614 .575 1.738 2.478 1.915 1.937 2.584 80 428 1.391 .88 110 4130 8850 41 52 298 309 0 3545 421 3125 1.704 1548 1127 .587 2.43 .769 1.281
17 755 2165 193 430 562 1735 318 1157 215 521 125 727 0 0 1083 2529 134 377 48 61 40 50 2297 852 .324 3.087 5.816 2.869 2.908 2.735 52 221 3.029 .89 90 4310 8840 41 50 317 326 0 2123 422 1701 3.027 1134 713 .33 5.702 1.598 2.511
18 161 390 182 417 -21 -27 148 345 308 978 -34 -72 0 0 81 194 895 3811 0 0 0 0 -48 -106 null null null 2.031 2.123 2.591 80 370 4.338 .97 100 4450 8880 45 55 331 341 -50 382 409 -26 null 338 null null null null null
19 1625 5739 191 480 1434 5259 902 3481 471 1727 711 3001 0 0 2020 6755 1184 4971 38 34 21 21 6693 3712 .273 3.667 4.221 2.95 2.961 3.337 52 236 3.766 .91 80 4620 8890 47 55 349 357 0 5626 471 5156 3.595 3413 2942 .278 4.138 1.846 2.049
20 957 3173 98 227 859 2946 860 2417 112 263 762 2190 0 0 645 2100 41 117 100 100 91 100 3805 2952 .292 3.43 2.874 3.85 3.877 1.876 12 20 2.714 .91 40 4740 8840 44 48 363 367 0 3111 223 2888 3.362 2370 2147 .297 2.818 1.749 1.494

Total number of rows: 37632

Table truncated, full table size 8751 Kbytes.




Supplementary data files not provided

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