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Sample GSM84853 Query DataSets for GSM84853
Status Public on Nov 23, 2005
Title s3861, p529, 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 s3861, p529, Pax whole blood
Organism Homo sapiens
Characteristics s3861, p529, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23036.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
1 964 1357 140 151 824 1206 991 1383 142 160 851 1232 0 0 279 339 28 59 100 100 100 100 2030 2083 .683 1.464 1.448 1.494 1.432 1.271 80 490 1.448 .96 110 2310 8440 24 35 53 64 0 1234 137 1096 1.331 1257 1120 .752 1.316 .412 .396
2 1538 2507 140 155 1398 2352 1606 2627 143 162 1466 2472 0 0 379 590 32 61 100 100 100 100 3750 3938 .594 1.682 1.686 1.712 1.69 1.365 80 454 1.691 .96 110 2470 8440 24 35 69 80 0 2279 141 2138 1.529 2388 2247 .654 1.533 .613 .616
3 789 1532 145 154 644 1378 938 1771 147 164 793 1617 0 0 467 754 35 56 85 97 85 92 2022 2410 .467 2.14 2.039 2.204 1.988 1.794 80 404 2.069 .91 110 2630 8440 24 35 85 96 0 1393 140 1253 1.945 1610 1470 .514 1.854 .96 .89
4 923 1272 145 158 778 1114 834 1119 153 172 689 961 0 0 691 859 56 72 83 89 79 84 1892 1650 .698 1.432 1.395 1.301 1.415 2.162 120 521 1.366 .92 120 2790 8430 23 35 101 113 0 1156 144 1013 1.302 1017 874 .768 1.268 .38 .343
5 478 573 140 157 338 416 520 592 143 164 380 435 0 0 172 178 39 58 93 93 90 93 754 815 .813 1.231 1.145 1.201 1.167 2.069 80 383 1.213 .87 110 2950 8440 24 35 117 128 0 521 143 378 1.119 538 395 .894 1.041 .162 .058
6 619 1482 138 145 481 1337 174 764 141 150 36 619 0 0 963 1865 46 56 49 66 45 58 1818 655 .36 2.78 17.194 2.375 2.224 3.438 120 464 2.18 .92 130 3110 8440 23 36 132 145 -100 1347 132 1215 2.527 695 563 .396 15.631 1.337 3.966
7 1490 2312 136 129 1354 2183 1545 2281 135 136 1409 2152 0 0 605 911 45 50 98 100 98 98 3537 3561 .62 1.612 1.527 1.646 1.59 1.498 80 335 1.604 .96 110 3260 8440 24 35 148 159 0 2102 117 1985 1.466 2074 1956 .682 1.388 .552 .474
8 1075 1402 136 130 939 1272 1208 1507 137 139 1072 1377 0 0 445 495 25 49 95 100 95 98 2211 2449 .738 1.355 1.285 1.44 1.367 1.522 80 387 1.291 .93 110 3420 8440 24 35 164 175 0 1275 118 1156 1.231 1370 1252 .812 1.168 .3 .224
9 1473 1446 137 140 1336 1306 1706 1607 141 148 1569 1467 0 0 879 742 29 52 83 90 83 90 2642 3036 1.023 .978 .935 1.027 .952 2.686 80 417 .902 .93 110 3570 8440 24 35 179 190 0 1315 127 1187 .889 1461 1334 1.125 .85 -.17 -.234
10 1503 2501 139 141 1364 2360 1710 2334 140 147 1571 2193 0 0 857 1394 30 49 88 98 86 97 3724 3764 .578 1.73 1.396 2.058 1.779 2.172 80 379 1.747 .95 100 3740 8430 24 34 197 207 0 2274 128 2145 1.573 2122 1994 .636 1.269 .653 .344
11 1411 2137 140 144 1271 1993 1363 2146 142 148 1223 2002 0 0 312 418 29 46 100 100 100 100 3264 3225 .638 1.568 1.637 1.582 1.58 1.215 80 350 1.551 .96 100 3890 8430 24 34 212 222 0 1943 131 1812 1.426 1951 1820 .702 1.488 .511 .574
12 1520 2414 149 154 1371 2260 1555 2451 154 161 1406 2297 0 0 576 741 36 57 100 100 100 100 3631 3703 .607 1.648 1.634 1.739 1.714 1.388 80 413 1.601 .96 110 4040 8430 23 34 226 237 0 2195 140 2055 1.499 2228 2088 .667 1.485 .584 .571
13 1309 1877 149 145 1160 1732 1310 1891 152 155 1161 1746 0 0 369 388 35 58 100 100 100 100 2892 2907 .67 1.493 1.504 1.56 1.567 1.354 80 392 1.451 .96 100 4200 8430 24 34 243 253 0 1706 132 1575 1.357 1719 1587 .737 1.367 .441 .451
14 3329 4078 144 138 3185 3940 3672 4501 145 144 3528 4363 0 0 1864 2087 29 50 92 98 91 98 7125 7891 .808 1.237 1.237 1.504 1.263 2.09 80 390 1.212 .95 110 4360 8430 23 34 258 269 0 3707 125 3582 1.125 4092 3966 .889 1.124 .169 .169
15 1317 1949 140 135 1177 1814 1277 1876 141 140 1137 1741 0 0 1035 1192 26 49 90 99 87 96 2991 2878 .649 1.541 1.531 1.936 1.603 2.073 120 425 1.368 .95 120 4510 8430 23 35 273 285 0 1772 123 1649 1.401 1705 1583 .714 1.392 .487 .477
16 1682 5303 139 130 1543 5173 1836 5669 141 137 1697 5539 0 0 1134 3110 27 49 94 100 91 100 6716 7236 .298 3.353 3.264 3.632 3.4 1.663 120 438 3.248 .94 120 4670 8420 22 34 289 301 0 4821 118 4703 3.048 5154 5035 .328 2.967 1.608 1.569
17 2039 1212 134 124 1905 1088 1901 1131 136 131 1767 1007 0 0 1289 675 28 46 88 92 88 91 2993 2774 1.751 .571 .57 .591 .568 1.643 80 392 .538 .97 110 4830 8420 22 33 305 316 0 1102 113 989 .519 1028 915 1.926 .518 -.946 -.949
18 1479 2046 132 126 1347 1920 1604 2137 135 133 1472 2011 0 0 509 610 28 46 100 100 100 100 3267 3483 .702 1.425 1.366 1.483 1.42 1.327 80 391 1.395 .97 110 4980 8430 23 34 320 331 0 1860 115 1745 1.296 1943 1828 .772 1.242 .374 .313
19 394 286 133 130 261 156 180 163 135 136 47 33 0 0 447 310 28 47 60 45 43 36 417 80 1.673 .598 .702 .934 .723 3.198 80 367 .662 .91 100 5140 8430 24 34 337 347 -50 260 118 142 .543 148 30 1.84 .638 -.88 -.648
20 1717 1332 136 134 1581 1198 1789 1337 138 143 1653 1203 0 0 870 685 29 51 100 100 100 100 2779 2856 1.32 .758 .728 .778 .783 1.357 52 301 .766 .96 90 5290 8430 24 33 352 361 0 1211 122 1089 .689 1215 1094 1.452 .662 -.538 -.596

Total number of rows: 37632

Table truncated, full table size 8664 Kbytes.




Supplementary data files not provided
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