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Sample GSM84971 Query DataSets for GSM84971
Status Public on Nov 23, 2005
Title s6131, p903, 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 s6131, p903, Pax whole blood
Organism Homo sapiens
Characteristics s6131, p903, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23028.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
1 909 1644 133 151 776 1493 919 1571 135 159 786 1420 0 0 362 705 27 55 98 100 98 98 2269 2206 .52 1.924 1.807 1.893 1.878 1.428 80 468 1.963 .96 110 2170 8140 27 38 33 44 0 1337 123 1214 1.564 1277 1154 .639 1.469 .645 .555
2 1290 2517 129 146 1161 2371 1284 2617 130 154 1155 2471 0 0 445 822 25 53 98 100 98 100 3532 3626 .49 2.042 2.139 2.063 2.039 1.231 80 386 2.028 .97 100 2320 8140 28 38 49 59 0 2046 119 1928 1.66 2128 2009 .602 1.739 .731 .799
3 760 2162 126 147 634 2015 735 1934 128 155 609 1787 0 0 425 1249 25 57 95 98 90 97 2649 2396 .315 3.178 2.934 3.443 3.109 1.763 80 441 3.145 .96 110 2480 8140 27 38 64 75 0 1758 120 1638 2.584 1572 1453 .387 2.386 1.37 1.254
4 972 1595 126 145 846 1450 840 1453 129 152 714 1308 0 0 640 1040 25 55 87 98 86 95 2296 2022 .583 1.714 1.832 1.772 1.709 1.848 80 447 1.747 .94 110 2640 8140 27 38 80 91 0 1297 118 1179 1.393 1181 1063 .718 1.489 .479 .575
5 509 838 122 143 387 695 429 692 124 148 307 549 0 0 257 466 21 53 98 100 96 98 1082 856 .557 1.796 1.788 1.79 1.848 1.688 80 401 1.908 .91 100 2800 8140 28 38 97 107 0 681 116 565 1.46 563 446 .685 1.454 .546 .54
6 927 2085 120 139 807 1946 912 2159 122 146 792 2020 0 0 381 746 22 51 97 100 97 100 2753 2812 .415 2.411 2.551 2.532 2.539 1.488 80 412 2.37 .95 110 2960 8140 27 38 112 123 0 1695 113 1582 1.96 1755 1642 .51 2.074 .971 1.052
7 1276 2092 121 137 1155 1955 1403 2178 123 143 1282 2041 0 0 683 1051 25 50 87 100 87 98 3110 3323 .591 1.693 1.592 1.738 1.665 1.531 80 405 1.675 .97 110 3110 8140 27 38 127 138 0 1701 111 1589 1.376 1771 1659 .727 1.294 .461 .372
8 886 1311 125 145 761 1166 856 1184 126 153 731 1039 0 0 326 582 24 56 100 100 100 100 1927 1770 .653 1.532 1.421 1.506 1.484 1.368 80 403 1.609 .94 110 3270 8150 28 39 143 154 0 1066 118 948 1.246 963 845 .803 1.156 .317 .209
9 1183 1498 128 149 1055 1349 1248 1522 128 157 1120 1373 0 0 585 684 23 60 92 96 92 95 2404 2493 .782 1.279 1.226 1.297 1.24 1.673 120 460 1.24 .96 120 3430 8140 27 39 159 171 0 1218 121 1097 1.04 1237 1116 .962 .997 .056 -.005
10 1774 3110 127 145 1647 2965 1704 2930 138 153 1577 2785 0 0 832 1554 204 55 100 100 96 100 4612 4362 .555 1.8 1.766 1.766 1.78 1.241 80 344 1.828 .98 110 3580 8140 27 38 174 185 0 2528 118 2411 1.464 2382 2264 .683 1.436 .55 .522
11 1166 1871 124 150 1042 1721 1035 1804 127 158 911 1654 0 0 807 1233 24 55 93 98 90 95 2763 2565 .605 1.652 1.816 1.782 1.717 1.685 120 428 1.607 .96 120 3740 8130 26 38 190 202 0 1521 122 1399 1.343 1467 1345 .745 1.476 .425 .562
12 1401 2309 127 154 1274 2155 739 1545 128 160 612 1391 0 0 1547 2390 23 53 91 96 86 95 3429 2003 .591 1.692 2.273 2.128 1.853 2.067 120 401 1.619 .96 120 3900 8140 27 39 206 218 0 1877 125 1752 1.375 1256 1131 .727 1.848 .46 .886
13 1024 1726 128 154 896 1572 1133 1686 130 160 1005 1532 0 0 594 940 26 56 90 97 86 95 2468 2537 .57 1.754 1.524 2.092 1.848 2.02 80 400 1.718 .95 110 4050 8130 26 37 221 232 0 1403 125 1278 1.426 1371 1246 .701 1.239 .512 .31
14 3374 4741 125 156 3249 4585 3447 4404 130 163 3322 4248 0 0 1926 2656 28 57 100 100 97 100 7834 7570 .709 1.411 1.279 1.588 1.435 1.631 80 400 1.392 .98 110 4210 8140 27 38 237 248 0 3854 127 3728 1.147 3580 3454 .872 1.04 .198 .056
15 1485 2534 122 150 1363 2384 1280 2177 125 165 1158 2027 0 0 1020 1636 28 84 97 100 94 99 3747 3185 .572 1.749 1.75 2.016 1.784 1.885 120 468 1.705 .97 120 4370 8140 27 39 253 265 0 2060 122 1938 1.422 1770 1648 .703 1.423 .508 .509
16 1930 11373 122 153 1808 11220 1956 11086 126 177 1834 10933 0 0 683 3385 30 113 98 100 96 100 13028 12767 .161 6.206 5.961 6.6 6.359 1.429 80 419 6.016 .98 110 4530 8130 26 37 269 280 0 9246 124 9122 5.045 9013 8889 .198 4.847 2.335 2.277
17 1440 1068 119 152 1321 916 1299 1048 122 166 1180 896 0 0 807 535 26 89 96 96 95 95 2237 2076 1.442 .693 .759 .746 .701 1.778 80 364 .661 .94 100 4680 8130 27 37 285 295 0 868 124 745 .564 852 728 1.774 .617 -.827 -.696
18 1093 1987 121 147 972 1840 1082 1960 122 155 961 1813 0 0 643 1190 22 56 88 92 88 91 2812 2774 .528 1.893 1.887 1.943 1.85 1.698 80 433 1.907 .96 110 4840 8130 26 37 300 311 0 1615 120 1496 1.539 1593 1474 .65 1.534 .622 .617
19 260 220 122 153 138 67 155 196 124 159 33 43 0 0 356 134 26 56 55 41 40 18 205 76 2.06 .486 1.303 1.133 1 2.945 80 396 .357 .74 100 5000 8140 28 38 317 327 -50 179 124 54 .395 159 35 2.533 1.059 -1.341 .083
20 1341 1522 126 161 1215 1361 1064 939 128 163 938 778 0 0 901 1346 27 53 94 96 94 96 2576 1716 .893 1.12 .829 .974 1.025 1.652 52 294 1.299 .94 90 5170 8140 28 37 334 343 0 1237 131 1107 .911 763 633 1.098 .674 -.135 -.568

Total number of rows: 37632

Table truncated, full table size 8583 Kbytes.




Supplementary data files not provided
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