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Sample GSM84969 Query DataSets for GSM84969
Status Public on Nov 23, 2005
Title s8594, p825, 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 s8594, p825, Pax whole blood
Organism Homo sapiens
Characteristics s8594, p825, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23027.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
1 898 1632 151 252 747 1380 880 1572 155 267 729 1320 0 0 242 508 34 97 100 100 100 100 2127 2049 .541 1.847 1.811 1.825 1.883 1.271 80 476 1.961 .95 110 2190 8060 33 44 37 48 0 1295 200 1095 1.466 1248 1048 .682 1.437 .552 .523
2 1339 2441 151 245 1188 2196 1400 2369 159 296 1249 2124 0 0 467 761 102 665 100 100 98 87 3384 3373 .541 1.848 1.701 1.911 1.855 1.332 80 478 2.414 .86 110 2350 8060 33 44 53 64 0 1937 194 1743 1.467 1880 1686 .682 1.35 .553 .433
3 785 1804 148 240 637 1564 765 1680 155 291 617 1440 0 0 293 713 104 680 98 92 92 53 2201 2057 .407 2.455 2.334 2.471 2.43 1.321 80 454 2.437 .96 110 2520 8060 33 44 70 81 0 1432 190 1241 1.949 1333 1143 .513 1.852 .962 .889
4 1112 2028 147 249 965 1779 1129 1747 153 260 982 1498 0 0 379 829 42 101 100 100 100 100 2744 2480 .542 1.844 1.525 1.803 1.794 1.311 80 464 1.941 .95 110 2670 8050 32 43 85 96 0 1610 198 1412 1.463 1387 1189 .683 1.211 .549 .276
5 714 1675 150 236 564 1439 731 1664 153 251 581 1428 0 0 237 800 32 97 100 100 97 97 2003 2009 .392 2.551 2.458 2.411 2.439 1.607 80 369 2.949 .92 100 2840 8060 34 44 103 113 0 1329 187 1142 2.025 1321 1133 .494 1.951 1.018 .964
6 1070 2977 150 243 920 2734 1063 2973 152 254 913 2730 0 0 294 747 30 90 100 100 100 100 3654 3643 .337 2.972 2.99 3.027 2.931 1.244 80 389 2.929 .97 110 2990 8060 33 44 117 128 0 2363 193 2170 2.359 2360 2167 .424 2.373 1.238 1.247
7 1600 2955 151 268 1449 2687 1580 2767 154 277 1429 2499 0 0 550 1028 33 107 100 100 100 100 4136 3928 .539 1.854 1.749 1.878 1.865 1.345 80 401 1.878 .96 110 3140 8050 32 43 132 143 0 2345 213 2133 1.472 2196 1983 .679 1.388 .558 .473
8 1178 2140 152 272 1026 1868 1165 2130 156 286 1013 1858 0 0 312 700 33 109 100 100 100 100 2894 2871 .549 1.821 1.834 1.782 1.794 1.268 80 412 1.904 .96 110 3290 8060 33 44 147 158 0 1698 216 1483 1.445 1690 1475 .692 1.456 .531 .542
9 1660 2095 152 277 1508 1818 1768 2030 157 288 1616 1753 0 0 622 755 36 103 97 98 96 98 3326 3369 .829 1.206 1.085 1.3 1.236 1.589 80 379 1.235 .95 100 3460 8050 33 43 165 175 0 1663 220 1443 .957 1611 1391 1.045 .861 -.064 -.216
10 1576 2935 154 269 1422 2666 1608 2914 160 282 1454 2645 0 0 865 1419 38 105 93 98 91 98 4088 4099 .533 1.875 1.819 2.019 1.853 1.614 80 432 1.849 .97 110 3610 8050 32 43 179 190 0 2329 213 2116 1.488 2313 2099 .672 1.444 .573 .53
11 1426 2707 154 283 1272 2424 1445 2550 159 298 1291 2267 0 0 408 747 38 108 100 100 100 100 3696 3558 .525 1.906 1.756 1.944 1.915 1.294 80 424 1.952 .95 110 3770 8050 32 43 195 206 0 2148 225 1924 1.512 2024 1799 .661 1.394 .597 .479
12 1458 2952 150 300 1308 2652 1329 2488 157 309 1179 2188 0 0 830 1660 38 109 96 98 95 98 3960 3367 .493 2.028 1.856 2.164 2.125 1.644 80 335 2.042 .95 100 3930 8060 34 44 212 222 0 2343 238 2105 1.609 1975 1737 .621 1.473 .686 .559
13 1298 2455 149 296 1149 2159 1281 2464 155 312 1132 2168 0 0 308 582 39 109 100 100 100 100 3308 3300 .532 1.879 1.915 1.882 1.867 1.223 80 399 1.897 .97 110 4080 8050 32 43 226 237 0 1948 235 1713 1.491 1956 1721 .671 1.52 .577 .604
14 3308 4191 153 300 3155 3891 3296 4126 155 316 3143 3826 0 0 1253 1439 37 106 100 100 100 100 7046 6969 .811 1.233 1.217 1.264 1.231 1.255 80 413 1.201 .97 110 4240 8050 32 43 242 253 0 3326 238 3088 .979 3275 3037 1.022 .966 -.031 -.05
15 1780 3457 149 310 1631 3147 1666 3309 154 319 1517 2999 0 0 601 1039 36 101 100 100 100 100 4778 4516 .518 1.929 1.977 1.959 1.92 1.237 80 366 1.898 .97 100 4400 8050 33 43 259 269 0 2744 246 2498 1.531 2626 2380 .653 1.569 .615 .65
16 1880 5442 146 295 1734 5147 1899 5651 153 314 1753 5356 0 0 542 1471 39 145 100 100 100 100 6881 7109 .337 2.968 3.055 3.009 3.011 1.211 80 406 2.937 .98 110 4550 8040 31 42 273 284 0 4319 234 4085 2.356 4485 4251 .424 2.425 1.236 1.278
17 1949 1765 146 287 1803 1478 1811 1362 151 311 1665 1075 0 0 816 1080 40 154 100 100 100 98 3281 2740 1.22 .82 .646 .715 .699 1.488 80 365 .964 .93 100 4700 8050 33 43 289 299 0 1401 228 1173 .651 1081 853 1.537 .512 -.62 -.965
18 1258 2815 147 288 1111 2527 1337 2799 152 307 1190 2511 0 0 498 1171 37 111 98 100 98 100 3638 3701 .44 2.275 2.11 2.253 2.254 1.292 80 422 2.369 .96 110 4860 8050 32 43 304 315 0 2234 229 2006 1.805 2221 1993 .554 1.675 .852 .744
19 303 393 149 289 154 104 195 299 154 304 46 10 0 0 355 320 36 107 55 26 40 16 258 56 1.481 .675 .217 1.304 1.424 4.05 80 367 .969 .74 100 5020 8050 33 43 321 331 -50 312 229 83 .536 237 8 1.866 .173 -.9 -2.535
20 2201 3668 159 291 2042 3377 1954 2589 165 308 1795 2298 0 0 1567 3321 45 111 96 94 94 90 5419 4093 .605 1.654 1.28 1.49 1.61 2.326 52 247 1.983 .92 80 5170 8040 33 41 337 345 0 2911 231 2680 1.313 2055 1824 .762 1.016 .392 .023

Total number of rows: 37632

Table truncated, full table size 8665 Kbytes.




Supplementary data files not provided
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