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Sample GSM84838 Query DataSets for GSM84838
Status Public on Nov 23, 2005
Title s9563, p582, 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 s9563, p582, Pax whole blood
Organism Homo sapiens
Characteristics s9563, p582, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23031.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
1 889 1687 139 206 750 1481 856 1596 143 221 717 1390 0 0 615 1136 27 93 80 92 80 88 2231 2107 .506 1.975 1.939 2.091 2.027 2.224 80 489 1.951 .95 110 2350 8370 27 38 49 60 0 1205 147 1058 1.41 1140 993 .709 1.385 .496 .47
2 1499 2739 140 201 1359 2538 1647 2907 145 219 1507 2706 0 0 625 1073 30 89 96 98 95 98 3897 4213 .535 1.868 1.796 1.938 1.821 1.735 80 432 1.864 .96 110 2510 8370 27 38 65 76 0 1956 144 1813 1.334 2076 1933 .75 1.283 .416 .359
3 853 2445 140 202 713 2243 719 1950 142 215 579 1748 0 0 578 2038 26 69 91 100 87 98 2956 2327 .318 3.146 3.019 3.476 2.937 1.867 120 468 4.419 .73 120 2670 8370 27 39 81 93 0 1746 144 1602 2.247 1393 1249 .445 2.156 1.168 1.109
4 1184 2078 137 210 1047 1868 1291 2090 142 218 1154 1880 0 0 643 1193 28 74 98 97 96 95 2915 3034 .56 1.784 1.629 1.861 1.821 2.083 80 413 1.848 .94 110 2820 8370 27 38 96 107 0 1484 150 1334 1.274 1493 1343 .785 1.164 .35 .219
5 731 1158 142 207 589 951 749 1088 151 221 607 881 0 0 202 368 53 85 100 100 100 100 1540 1488 .619 1.615 1.451 1.629 1.645 1.435 52 312 1.658 .92 90 2970 8360 27 36 112 121 0 827 148 679 1.153 777 629 .867 1.037 .206 .052
6 808 1894 138 204 670 1690 691 1634 148 242 553 1430 0 0 626 1389 67 295 80 77 73 71 2360 1983 .396 2.522 2.586 2.633 2.554 2.001 120 462 2.568 .91 120 3140 8370 27 39 128 140 0 1353 146 1207 1.802 1167 1021 .555 1.847 .849 .885
7 1393 2558 137 201 1256 2357 1356 2531 143 214 1219 2330 0 0 591 959 64 95 97 100 96 100 3613 3549 .533 1.877 1.911 1.898 1.828 1.501 80 381 1.861 .95 110 3290 8360 26 37 143 154 0 1827 144 1684 1.34 1808 1664 .746 1.365 .423 .449
8 1065 1845 138 198 927 1647 1055 1820 145 213 917 1622 0 0 240 466 60 93 100 100 100 100 2574 2539 .563 1.777 1.769 1.76 1.743 1.237 80 433 1.807 .96 110 3450 8370 27 38 159 170 0 1318 141 1176 1.269 1300 1159 .788 1.263 .344 .337
9 1538 2133 136 197 1402 1936 1691 2134 142 208 1555 1937 0 0 655 768 55 82 93 100 93 97 3338 3492 .724 1.381 1.246 1.53 1.387 1.851 80 406 1.345 .96 110 3610 8360 26 37 175 186 0 1524 141 1383 .986 1524 1384 1.014 .89 -.02 -.169
10 1564 2943 136 192 1428 2751 1381 2565 148 212 1245 2373 0 0 975 1547 74 103 92 100 92 100 4179 3618 .519 1.926 1.906 2.164 1.967 1.774 80 349 1.825 .95 100 3770 8360 27 37 192 202 0 2102 137 1965 1.376 1832 1695 .727 1.361 .461 .445
11 1529 2191 136 194 1393 1997 1711 2267 158 228 1575 2073 0 0 896 1168 110 168 83 90 78 83 3390 3648 .698 1.434 1.316 1.488 1.483 2.005 80 435 1.449 .93 110 3920 8350 25 36 206 217 0 1565 139 1426 1.024 1619 1481 .977 .94 .034 -.089
12 1358 2613 138 200 1220 2413 1156 2151 162 227 1018 1951 0 0 1021 1876 130 155 82 95 77 87 3633 2969 .506 1.978 1.917 2.381 2.022 2.012 80 431 1.944 .96 110 4090 8360 26 37 223 234 0 1866 143 1724 1.413 1536 1394 .708 1.369 .499 .453
13 1201 1968 143 206 1058 1762 1230 1873 214 251 1087 1667 0 0 626 837 399 233 85 96 65 92 2820 2754 .6 1.665 1.534 1.624 1.656 1.874 80 374 1.601 .94 110 4240 8370 27 38 238 249 0 1406 147 1259 1.19 1338 1191 .841 1.095 .25 .131
14 2850 3756 139 210 2711 3546 2337 3145 141 216 2198 2935 0 0 2246 2865 28 77 97 99 95 98 6257 5133 .765 1.308 1.335 1.399 1.282 1.923 120 423 1.303 .96 120 4390 8370 27 39 253 265 0 2683 150 2533 .934 2246 2096 1.07 .954 -.098 -.068
15 1654 2763 140 211 1514 2552 1778 2903 145 222 1638 2692 0 0 879 1377 48 87 91 98 88 98 4066 4330 .593 1.686 1.643 1.99 1.712 2.097 80 369 1.683 .95 110 4540 8370 27 38 268 279 0 1974 151 1823 1.204 2074 1923 .831 1.174 .268 .231
16 1286 6974 141 214 1145 6760 1317 7755 145 222 1176 7541 0 0 716 3128 42 74 95 100 93 100 7905 8717 .169 5.904 6.412 6.567 5.902 1.671 120 552 5.647 .95 130 4700 8360 25 38 283 296 0 4981 153 4829 4.217 5539 5386 .237 4.58 2.076 2.195
17 1573 1258 140 216 1433 1042 1477 1183 141 220 1337 967 0 0 512 393 27 68 100 100 100 100 2475 2304 1.375 .727 .723 .726 .748 1.277 80 393 .721 .95 110 4860 8370 27 38 300 311 0 899 154 744 .519 845 691 1.925 .517 -.945 -.953
18 1416 2609 136 203 1280 2406 1452 2567 138 215 1316 2364 0 0 513 845 26 72 98 100 98 100 3686 3680 .532 1.88 1.796 1.911 1.922 1.384 80 391 1.879 .95 110 5020 8370 27 38 316 327 0 1864 145 1719 1.343 1834 1689 .745 1.283 .425 .36
19 264 307 136 209 128 98 181 228 137 224 45 19 0 0 275 229 25 78 61 37 46 20 226 64 1.306 .766 .422 1.101 1.154 3.722 80 350 .897 .77 100 5170 8370 28 38 332 342 -50 219 149 70 .547 163 14 1.829 .302 -.871 -1.729
20 1205 1355 137 220 1068 1135 1119 1308 139 230 982 1088 0 0 667 622 27 82 100 100 100 98 2203 2070 .941 1.063 1.108 1.123 1.031 1.705 52 304 1.018 .9 90 5320 8360 27 36 347 356 0 968 157 811 .759 934 777 1.317 .791 -.398 -.338

Total number of rows: 37632

Table truncated, full table size 8706 Kbytes.




Supplementary data files not provided
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