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Sample GSM84834 Query DataSets for GSM84834
Status Public on Nov 23, 2005
Title s7872, p316, 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 s7872, p316, Pax whole blood
Organism Homo sapiens
Characteristics s7872, p316, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23030.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
1 919 1586 170 191 749 1395 903 1598 183 208 733 1407 0 0 301 520 63 87 98 100 97 100 2144 2140 .537 1.862 1.92 1.942 1.832 1.374 80 410 1.936 .93 100 1930 8120 32 42 35 45 0 1133 136 996 1.33 1141 1005 .752 1.371 .412 .455
2 1311 3064 135 145 1176 2919 1339 3298 138 153 1204 3153 0 0 356 819 27 64 100 100 100 100 4095 4357 .403 2.482 2.619 2.506 2.494 1.167 80 451 2.459 .98 110 2090 8110 30 41 50 61 0 2189 104 2085 1.773 2356 2252 .564 1.871 .826 .903
3 933 3169 134 144 799 3025 967 3241 138 156 833 3097 0 0 342 1124 31 101 100 100 100 100 3824 3930 .264 3.786 3.718 3.943 3.825 1.343 80 436 3.737 .97 110 2240 8110 30 41 65 76 0 2264 103 2161 2.704 2315 2212 .37 2.656 1.435 1.409
4 987 1855 130 138 857 1717 988 1813 133 146 858 1675 0 0 375 626 30 52 100 100 100 100 2574 2533 .499 2.004 1.952 2.093 2.057 1.269 80 365 1.933 .97 100 2390 8110 31 41 81 91 0 1325 99 1226 1.431 1295 1196 .699 1.394 .517 .48
5 525 717 124 136 401 581 502 706 128 142 378 570 0 0 217 269 27 46 100 100 96 100 982 948 .69 1.449 1.508 1.581 1.47 1.548 80 378 1.424 .93 100 2550 8110 31 41 97 107 0 512 97 415 1.035 504 407 .966 1.077 .05 .107
6 1063 3446 126 136 937 3310 1068 3464 129 143 942 3328 0 0 463 996 29 53 98 100 98 100 4247 4270 .283 3.533 3.533 3.831 3.553 1.478 80 421 3.452 .94 110 2710 8110 30 41 112 123 0 2461 97 2364 2.523 2474 2377 .396 2.524 1.335 1.335
7 1652 3297 126 137 1526 3160 1680 3266 128 144 1554 3129 0 0 487 798 26 56 100 100 100 100 4686 4683 .483 2.071 2.014 2.143 2.061 1.327 80 416 2.026 .98 110 2860 8110 30 41 127 138 0 2355 98 2257 1.479 2333 2235 .676 1.438 .565 .524
8 1034 1682 126 137 908 1545 1020 1609 128 143 894 1472 0 0 321 453 27 50 100 100 100 100 2453 2366 .588 1.702 1.647 1.745 1.649 1.256 80 401 1.671 .96 110 3020 8110 30 41 143 154 0 1201 98 1104 1.215 1149 1051 .823 1.176 .281 .234
9 1473 2134 127 136 1346 1998 1542 2189 127 142 1415 2053 0 0 463 589 28 49 96 98 96 98 3344 3468 .674 1.484 1.451 1.519 1.464 1.318 80 390 1.454 .97 110 3170 8110 30 41 158 169 0 1524 97 1427 1.06 1564 1466 .943 1.036 .084 .052
10 1590 2642 119 140 1471 2502 1555 2536 122 144 1436 2396 0 0 648 886 30 53 100 100 100 100 3973 3832 .588 1.701 1.669 1.795 1.658 1.372 80 349 1.632 .97 100 3330 8110 31 41 175 185 0 1887 100 1787 1.215 1811 1711 .823 1.192 .281 .253
11 1383 2244 120 140 1263 2104 1355 2258 122 148 1235 2118 0 0 396 475 30 58 100 100 100 100 3367 3353 .6 1.666 1.715 1.722 1.617 1.28 80 406 1.638 .97 110 3480 8100 29 40 189 200 0 1603 100 1503 1.19 1613 1513 .84 1.225 .251 .293
12 1171 2174 119 138 1052 2036 948 1822 121 147 829 1684 0 0 728 1195 27 55 95 100 95 100 3088 2513 .517 1.935 2.031 2.09 2.023 1.453 80 398 1.821 .97 110 3630 8110 30 41 204 215 0 1553 99 1454 1.382 1301 1203 .723 1.451 .467 .537
13 873 1522 119 139 754 1383 900 1511 121 147 781 1372 0 0 372 618 27 53 96 97 95 97 2137 2153 .545 1.834 1.757 1.954 1.869 1.839 80 411 1.777 .97 110 3790 8110 30 41 220 231 0 1087 99 988 1.31 1079 980 .763 1.255 .39 .327
14 4198 5105 117 144 4081 4961 4504 5504 122 156 4387 5360 0 0 1592 1688 29 56 100 100 100 100 9042 9747 .823 1.216 1.222 1.308 1.186 1.55 80 396 1.174 .97 110 3950 8100 29 40 236 247 0 3646 103 3544 .868 3931 3829 1.152 .873 -.204 -.196
15 1015 1848 122 148 893 1700 1101 1727 126 157 979 1579 0 0 614 969 30 56 89 97 86 97 2593 2558 .525 1.904 1.613 2.148 1.817 2.009 120 412 1.797 .97 120 4110 8100 29 41 252 264 0 1320 106 1214 1.36 1234 1128 .735 1.152 .443 .204
16 1581 11424 126 148 1455 11276 1624 12274 130 155 1498 12126 0 0 921 5544 31 53 89 100 88 100 12731 13624 .129 7.75 8.095 8.632 7.847 1.612 120 413 7.346 .97 120 4270 8100 29 41 268 280 0 8160 106 8054 5.536 8767 8661 .181 5.782 2.469 2.532
17 1445 1161 122 145 1323 1016 1457 1120 131 158 1335 975 0 0 994 656 49 66 87 92 83 90 2339 2310 1.302 .768 .73 .992 .775 2.09 80 399 .702 .97 110 4410 8090 28 39 282 293 0 829 104 726 .549 800 696 1.823 .522 -.866 -.939
18 1716 2473 119 140 1597 2333 1852 2633 126 152 1733 2493 0 0 750 927 51 65 96 100 95 98 3930 4226 .685 1.461 1.439 1.541 1.449 1.37 80 392 1.416 .97 100 4580 8100 30 40 300 310 0 1766 100 1666 1.043 1881 1781 .958 1.028 .061 .039
19 345 262 120 142 225 120 172 200 123 150 52 58 0 0 414 221 31 56 61 51 43 25 345 110 1.875 .533 1.115 .729 .7 2.913 80 366 .512 .87 100 4740 8100 30 40 316 326 -50 187 101 86 .381 143 41 2.625 .797 -1.392 -.328
20 1451 1271 122 141 1329 1130 1276 1230 125 150 1154 1089 0 0 896 668 28 54 98 98 98 96 2459 2243 1.176 .85 .944 .879 .849 1.334 52 289 .809 .96 90 4890 8100 30 39 331 340 0 908 101 807 .607 879 778 1.647 .674 -.719 -.569

Total number of rows: 37632

Table truncated, full table size 8688 Kbytes.




Supplementary data files not provided
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