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Sample GSM84966 Query DataSets for GSM84966
Status Public on Nov 23, 2005
Title s9797, p635, 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 s9797, p635, Pax whole blood
Organism Homo sapiens
Characteristics s9797, p635, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23025.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
1 872 1314 167 173 705 1141 898 1360 171 180 731 1187 0 0 427 542 32 64 90 98 90 96 1846 1918 .618 1.618 1.624 1.793 1.608 1.712 80 383 1.48 .95 100 2050 8170 29 39 29 39 0 1051 138 913 1.295 1088 950 .772 1.299 .373 .377
2 1225 2254 169 173 1056 2081 1283 2403 172 178 1114 2230 0 0 359 596 33 60 100 100 100 100 3137 3344 .507 1.971 2.002 2.047 1.932 1.402 80 462 1.944 .97 110 2200 8160 27 38 43 54 0 1803 138 1665 1.577 1922 1784 .634 1.601 .657 .679
3 891 2159 167 173 724 1986 878 2147 171 178 711 1974 0 0 422 852 34 57 92 100 92 100 2710 2685 .365 2.743 2.776 2.842 2.631 1.349 80 388 2.558 .96 100 2370 8170 29 39 61 71 0 1727 138 1589 2.194 1718 1579 .456 2.221 1.134 1.151
4 1079 1676 166 166 913 1510 1029 1682 169 173 863 1516 0 0 805 964 32 62 83 92 82 90 2423 2379 .605 1.654 1.757 1.762 1.738 2.076 80 452 1.48 .93 110 2530 8160 27 38 76 87 0 1341 133 1208 1.323 1346 1213 .756 1.405 .404 .491
5 511 580 164 162 347 418 446 530 167 171 282 368 0 0 315 309 32 55 87 88 83 86 765 650 .83 1.205 1.305 1.242 1.17 1.784 80 357 1.111 .9 100 2680 8170 29 39 92 102 0 464 130 334 .964 424 294 1.038 1.044 -.053 .062
6 1040 2469 161 171 879 2298 1107 2533 164 181 946 2362 0 0 388 736 31 65 95 100 93 100 3177 3308 .383 2.614 2.497 2.7 2.594 1.384 80 396 2.479 .95 110 2840 8160 27 38 107 118 0 1975 137 1838 2.091 2026 1890 .478 1.997 1.065 .998
7 1472 2504 164 172 1308 2332 1458 2320 165 184 1294 2148 0 0 1004 1509 31 72 86 99 84 98 3640 3442 .561 1.783 1.66 2.112 1.814 1.934 120 440 1.675 .97 120 3000 8160 27 39 123 135 0 2003 138 1866 1.426 1856 1718 .701 1.328 .512 .409
8 1077 1493 163 172 914 1321 1105 1474 164 179 942 1302 0 0 275 383 32 66 100 100 100 100 2235 2244 .692 1.445 1.382 1.465 1.401 1.321 80 359 1.449 .96 110 3160 8170 28 39 139 150 0 1194 138 1057 1.156 1179 1042 .865 1.106 .209 .145
9 1794 2287 160 160 1634 2127 1882 2274 165 171 1722 2114 0 0 809 707 67 59 98 100 97 100 3761 3836 .768 1.302 1.228 1.438 1.309 1.555 80 404 1.197 .91 110 3310 8160 27 38 154 165 0 1830 128 1702 1.041 1819 1691 .96 .982 .058 -.026
10 2112 3662 163 169 1949 3493 2083 3242 196 180 1920 3073 0 0 996 1592 321 67 96 100 91 100 5442 4993 .558 1.792 1.601 1.921 1.872 1.456 80 429 1.745 .94 110 3470 8150 26 37 170 181 0 2930 135 2794 1.434 2594 2458 .697 1.28 .52 .357
11 1568 2573 166 178 1402 2395 1697 2749 245 190 1531 2571 0 0 695 1014 741 77 81 100 52 98 3797 4102 .585 1.708 1.679 1.78 1.682 1.444 80 399 1.397 .75 110 3630 8160 27 38 186 197 0 2058 142 1916 1.367 2199 2057 .732 1.343 .451 .426
12 1931 3328 163 186 1768 3142 1956 3378 226 196 1793 3192 0 0 1156 1778 685 73 82 100 62 93 4910 4985 .563 1.777 1.78 1.841 1.849 1.362 80 419 1.708 .92 110 3780 8150 26 37 201 212 0 2662 149 2514 1.422 2702 2554 .703 1.424 .508 .51
13 1149 1933 164 194 985 1739 1259 2031 170 202 1095 1837 0 0 603 876 54 68 86 100 85 96 2724 2932 .566 1.765 1.678 1.923 1.758 1.825 80 433 1.677 .97 110 3940 8150 26 37 217 228 0 1546 155 1391 1.412 1625 1470 .708 1.342 .498 .424
14 4160 4746 164 200 3996 4546 4267 4433 168 215 4103 4233 0 0 3150 2874 35 79 91 100 90 97 8542 8336 .879 1.138 1.032 1.433 1.168 1.947 80 419 1.049 .95 110 4090 8150 26 37 232 243 0 3797 160 3637 .91 3546 3386 1.099 .825 -.136 -.277
15 1982 3463 164 214 1818 3249 1971 3524 173 228 1807 3310 0 0 860 1057 73 85 96 100 96 100 5067 5117 .56 1.787 1.832 1.911 1.877 1.443 80 405 1.703 .95 110 4250 8150 26 37 248 259 0 2770 171 2599 1.43 2819 2648 .699 1.465 .516 .551
16 1556 5005 168 212 1388 4793 1720 5662 175 227 1552 5450 0 0 743 2132 71 85 94 100 90 100 6181 7002 .29 3.453 3.512 4.093 3.599 1.884 120 438 3.393 .96 120 4410 8150 26 38 264 276 0 4004 170 3834 2.763 4530 4360 .362 2.809 1.466 1.49
17 1686 884 170 212 1516 672 1623 854 172 231 1453 642 0 0 928 327 34 94 96 98 96 92 2188 2095 2.256 .443 .442 .462 .441 1.496 80 326 .404 .93 100 4560 8160 28 38 280 290 0 707 170 538 .355 683 514 2.82 .353 -1.496 -1.5
18 1220 2065 173 225 1047 1840 1251 2164 177 242 1078 1939 0 0 575 893 37 88 91 96 90 96 2887 3017 .569 1.757 1.799 1.731 1.723 1.597 80 410 1.725 .96 110 4720 8160 27 38 295 306 0 1652 180 1472 1.406 1731 1551 .711 1.439 .492 .525
19 340 326 172 220 168 106 183 248 179 235 11 28 0 0 568 256 84 89 23 38 15 18 274 39 1.585 .631 2.545 1.54 1.507 4.804 80 376 .43 .75 100 4880 8160 28 38 312 322 -50 261 176 85 .505 198 22 1.981 2.036 -.986 1.026
20 1460 941 181 224 1279 717 1340 834 219 249 1159 610 0 0 979 498 185 99 81 93 81 90 1996 1769 1.784 .561 .526 .655 .533 2.128 32 197 .491 .9 70 5020 8140 27 34 327 334 0 753 179 574 .448 667 488 2.23 .421 -1.157 -1.248

Total number of rows: 37632

Table truncated, full table size 8597 Kbytes.




Supplementary data files not provided
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