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Sample GSM84929 Query DataSets for GSM84929
Status Public on Nov 23, 2005
Title s55C, pNepal, Pax whole blood
Sample type RNA
 
Channel 1
Source name Stratagene Universal Human Reference RNA, amplified from provided total RNA by AW 11/01
Organism Homo sapiens
Characteristics Stratagene Universal Human Reference RNA, amplified from provided total RNA by AW 11/01
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name s55C, pNepal, Pax whole blood
Organism Homo sapiens
Characteristics s55C, pNepal, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23089.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 22, 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 GPL3121
Series (1)
GSE3649 Individuality and variation in gene expression patterns in human blood.

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
1 806 1735 145 359 661 1376 834 1505 149 363 689 1146 0 0 253 770 36 92 100 100 98 100 2037 1835 .48 2.082 1.663 2.019 1.813 1.545 80 442 2.528 .87 100 2010 8070 31 41 26 36 0 1434 297 1137 1.72 1244 947 .581 1.375 .783 .459
2 1150 2739 148 374 1002 2365 1157 2648 151 391 1009 2274 0 0 320 906 31 109 100 100 100 100 3367 3283 .424 2.36 2.254 2.378 2.223 1.401 80 412 2.478 .95 100 2180 8070 31 41 43 53 0 2264 309 1955 1.951 2188 1879 .513 1.863 .964 .897
3 887 2977 151 386 736 2591 846 2877 153 400 695 2491 0 0 239 777 35 113 100 100 100 100 3327 3186 .284 3.52 3.584 3.528 3.552 1.237 80 389 3.553 .96 100 2330 8080 32 42 58 68 0 2460 319 2141 2.909 2378 2059 .344 2.962 1.541 1.567
4 1097 2855 151 398 946 2457 1089 2633 155 406 938 2235 0 0 403 1348 45 127 100 100 100 100 3403 3173 .385 2.597 2.383 2.469 2.368 1.406 80 431 2.995 .93 110 2490 8080 31 42 73 84 0 2360 329 2031 2.146 2176 1847 .466 1.969 1.102 .978
5 1000 3543 166 439 834 3104 843 3266 183 498 677 2827 0 0 501 1641 74 287 100 98 100 98 3938 3504 .269 3.722 4.176 3.693 3.735 1.47 52 338 3.76 .95 90 2640 8060 30 39 89 98 0 2928 363 2565 3.076 2699 2336 .325 3.451 1.621 1.787
6 1016 3974 167 417 849 3557 990 3667 176 428 823 3250 0 0 349 1473 59 137 100 100 100 100 4406 4073 .239 4.19 3.949 4.179 4.218 1.231 80 432 4.392 .96 110 2800 8070 30 41 104 115 0 3284 345 2940 3.463 3031 2686 .289 3.264 1.792 1.706
7 1319 4502 154 392 1165 4110 1256 4284 156 367 1102 3892 0 0 611 2019 78 162 98 100 97 100 5275 4994 .283 3.528 3.532 3.583 3.604 1.33 80 330 3.586 .95 100 2960 8070 31 41 121 131 0 3721 324 3397 2.916 3540 3217 .343 2.919 1.544 1.545
8 1205 5650 148 413 1057 5237 1138 5278 153 429 990 4865 0 0 548 2712 77 274 100 100 100 100 6294 5855 .202 4.955 4.914 4.904 4.911 1.195 80 415 4.95 .98 110 3110 8070 30 41 135 146 0 4669 341 4328 4.095 4362 4021 .244 4.061 2.034 2.022
9 1467 2613 150 401 1317 2212 1500 2528 152 412 1350 2127 0 0 311 734 47 168 100 100 100 100 3529 3477 .595 1.68 1.576 1.642 1.629 1.208 80 426 1.836 .94 110 3270 8070 30 41 151 162 0 2160 331 1828 1.388 2089 1758 .72 1.302 .473 .381
10 1165 2945 154 381 1011 2564 1170 3026 164 386 1016 2645 0 0 310 757 58 123 100 100 100 100 3575 3661 .394 2.536 2.603 2.535 2.424 1.245 52 305 2.593 .96 90 3420 8060 30 39 167 176 0 2434 315 2119 2.096 2501 2186 .477 2.152 1.068 1.105
11 842 1658 147 361 695 1297 861 1679 150 361 714 1318 0 0 191 434 47 109 100 100 100 100 1992 2032 .536 1.866 1.846 1.833 1.843 1.233 80 402 1.997 .95 100 3580 8070 31 41 183 193 0 1370 298 1072 1.542 1388 1089 .648 1.526 .625 .609
12 1119 2530 151 346 968 2184 1173 2536 168 360 1022 2190 0 0 292 768 113 138 100 100 100 100 3152 3212 .443 2.256 2.143 2.209 2.263 1.263 52 311 2.376 .95 90 3750 8070 31 40 200 209 0 2091 286 1805 1.865 2096 1810 .536 1.771 .899 .825
13 943 1938 145 334 798 1604 975 1865 155 345 830 1531 0 0 255 601 100 145 100 100 96 98 2402 2361 .498 2.01 1.845 1.978 2.049 1.297 80 429 2.063 .94 110 3890 8080 31 42 213 224 0 1602 276 1326 1.661 1541 1265 .602 1.524 .732 .608
14 1665 2278 140 342 1525 1936 1677 2245 148 346 1537 1903 0 0 508 741 77 123 100 100 98 100 3461 3440 .788 1.27 1.238 1.275 1.21 1.369 80 419 1.296 .96 110 4060 8070 30 41 230 241 0 1883 283 1600 1.049 1855 1573 .953 1.023 .069 .033
15 1023 1569 138 346 885 1223 1090 1646 158 370 952 1300 0 0 245 462 104 154 100 100 100 98 2108 2252 .724 1.382 1.366 1.326 1.391 1.26 52 291 1.465 .95 90 4200 8060 30 39 245 254 0 1297 286 1011 1.142 1360 1074 .876 1.129 .192 .174
16 988 3588 135 350 853 3238 989 3678 147 370 854 3328 0 0 149 565 74 132 100 100 100 100 4091 4182 .263 3.796 3.897 3.795 3.831 1.161 80 446 3.886 .97 110 4350 8070 30 41 259 270 0 2965 289 2676 3.137 3040 2750 .319 3.221 1.649 1.687
17 1220 1193 135 364 1085 829 1256 1193 140 372 1121 829 0 0 299 340 30 95 100 100 100 100 1914 1950 1.309 .764 .74 .727 .719 1.317 80 441 .792 .94 110 4500 8070 30 41 274 285 0 986 301 685 .631 986 685 1.584 .611 -.663 -.71
18 747 1243 133 372 614 871 770 1210 137 379 637 838 0 0 216 367 31 90 100 100 100 100 1485 1475 .705 1.419 1.316 1.411 1.39 1.356 80 361 1.495 .95 100 4670 8070 31 41 292 302 0 1027 307 720 1.172 1000 693 .853 1.087 .229 .121
19 393 710 132 382 261 328 181 445 136 381 49 63 0 0 417 657 32 90 60 45 43 31 589 112 .796 1.257 1.286 2.019 2.119 3.565 80 376 1.664 .85 100 4820 8070 31 41 307 317 -50 587 316 271 1.039 368 52 .963 1.063 .055 .088
20 1074 1600 133 370 941 1230 980 1580 140 375 847 1210 0 0 438 733 35 88 100 100 100 100 2171 2057 .765 1.307 1.429 1.164 1.282 1.463 52 254 1.439 .95 80 4980 8080 33 41 324 332 0 1322 306 1017 1.08 1306 1000 .926 1.181 .111 .24

Total number of rows: 37632

Table truncated, full table size 8636 Kbytes.




Supplementary data files not provided
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