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Sample GSM84952 Query DataSets for GSM84952
Status Public on Nov 23, 2005
Title s8469, 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 s8469, p529, Pax whole blood
Organism Homo sapiens
Characteristics s8469, p529, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23098.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 1122 1983 190 227 932 1756 1163 1961 240 243 973 1734 0 0 466 821 948 89 53 100 2 100 2688 2707 .531 1.884 1.782 1.949 1.88 1.48 80 409 1.995 .93 100 2080 8770 37 47 36 46 0 1271 146 1126 1.208 1257 1112 .828 1.142 .272 .192
2 1418 3663 187 242 1231 3421 1466 3894 191 277 1279 3652 0 0 766 1782 49 252 93 96 90 91 4652 4931 .36 2.779 2.855 2.944 2.786 1.707 80 411 2.757 .95 100 2240 8760 36 46 52 62 0 2348 155 2193 1.781 2496 2341 .561 1.83 .833 .872
3 1216 3513 180 225 1036 3288 1230 3380 185 247 1050 3155 0 0 492 1245 41 116 100 100 100 100 4324 4205 .315 3.174 3.005 3.341 3.252 1.326 80 386 3.145 .96 100 2400 8780 38 48 68 78 0 2252 144 2108 2.034 2167 2022 .492 1.926 1.025 .946
4 1505 3362 180 221 1325 3141 1546 3348 188 239 1366 3127 0 0 755 1606 56 107 95 100 95 98 4466 4493 .422 2.371 2.289 2.612 2.335 1.568 80 437 2.359 .96 110 2560 8770 36 47 83 94 0 2155 142 2013 1.52 2146 2004 .658 1.467 .604 .553
5 984 1788 174 199 810 1589 981 1582 180 209 807 1383 0 0 258 743 43 70 100 100 100 100 2399 2190 .51 1.962 1.714 1.892 1.873 1.355 52 313 2.155 .92 90 2700 8760 36 45 98 107 0 1146 128 1019 1.258 1014 887 .795 1.099 .331 .136
6 1137 4575 174 190 963 4385 1125 4789 176 207 951 4599 0 0 400 1412 38 110 98 100 98 100 5348 5550 .22 4.553 4.836 4.814 4.633 1.355 80 405 4.644 .95 100 2870 8760 36 46 115 125 0 2933 122 2811 2.919 3070 2948 .343 3.1 1.545 1.632
7 1743 3914 171 187 1572 3727 1765 4071 177 208 1594 3884 0 0 805 1572 54 97 98 100 97 100 5299 5478 .422 2.371 2.437 2.552 2.301 1.515 80 365 2.426 .94 100 3030 8760 36 46 131 141 0 2509 120 2389 1.52 2610 2490 .658 1.562 .604 .643
8 1177 2101 170 184 1007 1917 1203 2090 177 210 1033 1906 0 0 310 447 67 129 100 100 100 100 2924 2939 .525 1.904 1.845 1.953 1.857 1.297 80 439 1.884 .95 110 3180 8760 35 46 145 156 0 1347 118 1229 1.22 1340 1222 .819 1.183 .287 .242
9 1618 2783 170 189 1448 2594 1714 2992 180 223 1544 2803 0 0 1029 1591 78 181 83 93 81 85 4042 4347 .558 1.791 1.815 2.097 1.777 1.816 80 367 1.711 .96 100 3350 8750 35 45 163 173 0 1784 121 1663 1.148 1918 1797 .871 1.164 .2 .219
10 1274 2409 170 190 1104 2219 1231 2374 180 217 1061 2184 0 0 468 798 93 164 100 100 100 100 3323 3245 .498 2.01 2.058 2.064 2.015 1.278 80 356 1.97 .97 100 3490 8770 37 47 177 187 0 1544 122 1422 1.288 1522 1400 .776 1.32 .366 .4
11 1359 2741 145 168 1214 2573 1343 2741 178 231 1198 2573 0 0 590 1071 242 372 96 100 90 98 3787 3771 .472 2.119 2.148 2.291 2.148 1.421 52 332 1.995 .95 90 3650 8780 38 47 193 202 0 1757 108 1649 1.359 1757 1649 .736 1.377 .442 .461
12 345 738 149 166 196 572 166 428 167 208 17 262 0 0 376 782 147 192 38 51 30 44 768 279 .343 2.918 15.412 1.822 1.536 2.438 52 242 2.265 .89 80 3840 8780 39 47 213 221 0 473 106 367 1.871 274 168 .535 9.879 .904 3.304
13 850 2320 171 190 679 2130 646 2061 189 227 475 1871 0 0 768 2031 125 190 65 80 61 77 2809 2346 .319 3.137 3.939 2.577 2.844 2.585 80 346 2.826 .93 100 3980 8780 38 48 226 236 0 1487 122 1365 2.011 1321 1199 .497 2.525 1.008 1.336
14 3185 3864 176 199 3009 3665 3437 3803 187 228 3261 3604 0 0 1562 1898 80 158 97 100 97 95 6674 6865 .821 1.218 1.105 1.281 1.179 1.432 80 439 1.229 .96 110 4130 8750 34 45 240 251 0 2477 128 2349 .781 2438 2310 1.281 .708 -.357 -.497
15 1198 1974 178 216 1020 1758 1213 2011 199 269 1035 1795 0 0 341 437 118 275 98 100 98 100 2778 2830 .58 1.724 1.734 1.823 1.702 1.503 52 314 1.799 .95 90 4290 8750 35 44 257 266 0 1265 138 1127 1.105 1289 1151 .905 1.112 .144 .153
16 1708 7908 182 230 1526 7678 1715 7804 202 320 1533 7574 0 0 426 1550 133 592 100 100 100 100 9204 9107 .199 5.031 4.941 5.149 5.159 1.302 80 458 5.082 .96 110 4450 8740 33 44 272 283 0 5069 147 4922 3.225 5003 4855 .31 3.167 1.689 1.663
17 1985 1784 179 219 1806 1565 1945 1758 191 267 1766 1539 0 0 665 495 85 415 100 100 100 96 3371 3305 1.154 .867 .871 .888 .833 1.398 80 380 .838 .92 100 4610 8760 36 46 289 299 0 1144 140 1003 .555 1127 987 1.8 .559 -.848 -.84
18 1553 4021 173 207 1380 3814 1575 4262 176 214 1402 4055 0 0 558 1298 40 67 100 100 100 100 5194 5457 .362 2.764 2.892 2.852 2.771 1.358 80 347 2.756 .97 100 4770 8760 36 46 305 315 0 2578 133 2445 1.772 2732 2599 .564 1.854 .825 .891
19 470 459 171 204 299 255 263 316 176 211 92 112 0 0 464 386 40 67 65 56 57 43 554 204 1.173 .853 1.217 1.003 1.008 2.444 80 361 .846 .85 100 4920 8760 36 46 320 330 -50 294 131 163 .547 203 72 1.829 .78 -.871 -.358
20 1320 1559 174 216 1146 1343 1315 1690 178 223 1141 1474 0 0 462 400 42 76 100 100 100 100 2489 2615 .853 1.172 1.292 1.233 1.185 1.429 52 256 1.157 .93 80 5080 8760 37 45 337 345 0 999 138 861 .751 1083 945 1.331 .828 -.413 -.272

Total number of rows: 37632

Table truncated, full table size 8660 Kbytes.




Supplementary data files not provided
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