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Sample GSM84956 Query DataSets for GSM84956
Status Public on Nov 23, 2005
Title s8031, p890, 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 s8031, p890, Pax whole blood
Organism Homo sapiens
Characteristics s8031, p890, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23020.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 1322 2076 225 285 1097 1791 1366 2125 235 297 1141 1840 0 0 510 836 59 88 98 98 98 98 2888 2981 .613 1.633 1.613 1.635 1.606 1.357 80 372 1.697 .94 100 2040 8500 27 37 17 27 0 1674 230 1444 1.317 1714 1484 .76 1.301 .397 .379
2 1804 3169 224 260 1580 2909 1679 3005 233 277 1455 2745 0 0 1059 1538 54 103 95 100 93 98 4489 4200 .543 1.841 1.887 1.981 1.922 1.452 80 465 1.763 .94 110 2210 8510 27 38 33 44 0 2556 210 2346 1.485 2423 2214 .673 1.521 .57 .605
3 1000 2270 227 264 773 2006 1008 2215 245 293 781 1951 0 0 598 1208 86 122 86 97 80 93 2779 2732 .385 2.595 2.498 2.874 2.494 1.909 80 451 2.299 .95 110 2370 8510 27 38 49 60 0 1831 213 1618 2.093 1786 1573 .478 2.015 1.065 1.01
4 2476 3891 226 280 2250 3611 1876 3168 237 299 1650 2888 0 0 1565 2284 69 99 100 100 100 100 5861 4538 .623 1.605 1.75 1.721 1.633 1.352 80 405 1.525 .97 100 2520 8500 27 37 65 75 0 3138 226 2912 1.294 2555 2329 .773 1.412 .372 .497
5 1779 2914 245 309 1534 2605 1424 2313 312 397 1179 2004 0 0 1308 1838 221 285 93 96 90 93 4139 3183 .589 1.698 1.7 1.832 1.814 1.461 32 196 1.563 .94 70 2660 8490 27 34 80 87 0 2350 249 2101 1.369 1865 1616 .73 1.371 .454 .455
6 1628 3976 229 305 1399 3671 1627 3874 258 356 1398 3569 0 0 689 1412 125 230 97 100 95 100 5070 4967 .381 2.624 2.553 2.776 2.651 1.395 80 455 2.656 .96 110 2830 8500 26 37 95 106 0 3206 246 2960 2.116 3124 2878 .473 2.059 1.081 1.042
7 2648 4098 229 292 2419 3806 2780 4249 236 316 2551 3957 0 0 1148 1507 58 144 98 100 97 100 6225 6508 .636 1.573 1.551 1.757 1.594 1.651 80 416 1.523 .97 110 2990 8490 25 36 111 122 0 3305 235 3069 1.269 3427 3191 .788 1.251 .344 .323
8 1615 2554 222 289 1393 2265 1559 2502 232 304 1337 2213 0 0 456 748 58 120 100 100 100 100 3658 3550 .615 1.626 1.655 1.631 1.6 1.23 80 379 1.706 .94 100 3150 8500 27 37 128 138 0 2060 233 1827 1.311 2018 1785 .763 1.335 .391 .417
9 3227 3249 219 286 3008 2963 3186 3173 227 297 2967 2887 0 0 1324 1108 50 104 100 100 100 100 5971 5854 1.015 .985 .973 1.02 .963 1.305 80 400 .957 .95 110 3310 8490 25 36 143 154 0 2620 231 2390 .794 2559 2328 1.259 .785 -.332 -.35
10 2737 3894 221 288 2516 3606 2495 3673 229 301 2274 3385 0 0 1274 1470 50 103 100 100 98 100 6122 5659 .698 1.433 1.489 1.559 1.42 1.55 80 386 1.358 .96 110 3460 8490 25 36 158 169 0 3140 232 2908 1.156 2962 2730 .865 1.2 .209 .264
11 2090 2901 225 296 1865 2605 2086 2915 233 319 1861 2619 0 0 1065 1086 67 184 95 97 93 95 4470 4480 .716 1.397 1.407 1.522 1.438 1.701 80 422 1.335 .92 110 3620 8490 25 36 174 185 0 2340 239 2101 1.126 2351 2112 .888 1.135 .172 .183
12 2285 3380 223 302 2062 3078 2015 3114 228 312 1792 2812 0 0 1242 1719 52 90 97 100 97 100 5140 4604 .67 1.493 1.569 1.499 1.465 1.297 80 365 1.461 .95 100 3780 8500 27 37 191 201 0 2726 244 2482 1.204 2511 2268 .831 1.265 .268 .34
13 1589 2234 227 291 1362 1943 1595 2222 232 303 1368 1931 0 0 481 639 52 101 98 100 98 100 3305 3299 .701 1.427 1.412 1.431 1.412 1.219 80 409 1.402 .96 110 3940 8500 26 37 206 217 0 1802 235 1567 1.15 1792 1557 .869 1.138 .202 .187
14 4746 5701 224 285 4522 5416 5069 5790 233 298 4845 5505 0 0 1701 1819 54 93 98 100 98 100 9938 10350 .835 1.198 1.136 1.226 1.187 1.32 80 400 1.185 .96 110 4090 8500 26 37 221 232 0 4598 230 4368 .966 4669 4440 1.035 .916 -.05 -.126
15 2369 3458 223 291 2146 3167 2240 3588 234 308 2017 3297 0 0 893 1004 66 105 100 100 98 100 5313 5314 .678 1.476 1.635 1.566 1.476 1.377 80 363 1.41 .96 100 4250 8500 27 37 238 248 0 2789 235 2554 1.19 2894 2659 .84 1.318 .251 .399
16 2280 10516 226 298 2054 10218 2076 10219 239 311 1850 9921 0 0 1069 3378 69 110 98 100 98 100 12272 11771 .201 4.975 5.363 5.205 5.181 1.367 80 407 4.869 .93 110 4400 8490 25 36 252 263 0 8481 240 8240 4.012 8241 8001 .249 4.325 2.004 2.113
17 2088 1546 227 306 1861 1240 2035 1455 235 312 1808 1149 0 0 806 554 52 99 100 100 98 100 3101 2957 1.501 .666 .636 .686 .671 1.449 80 349 .662 .94 100 4560 8500 27 37 269 279 0 1247 247 1000 .537 1173 927 1.861 .513 -.896 -.964
18 1577 2603 229 302 1348 2301 1480 2519 238 313 1251 2217 0 0 636 896 56 94 100 100 98 100 3649 3468 .586 1.707 1.772 1.821 1.611 1.631 80 445 1.665 .94 110 4710 8490 25 36 283 294 0 2099 244 1856 1.377 2031 1788 .726 1.429 .461 .515
19 382 391 229 305 153 86 237 311 239 314 8 6 0 0 407 269 55 93 33 21 23 16 239 14 1.779 .562 .75 .915 1.208 3.258 80 387 .591 .67 100 4890 8510 28 38 302 312 -50 315 246 69 .453 251 5 2.206 .605 -1.141 -.725
20 1972 2067 232 298 1740 1769 1709 1716 245 313 1477 1418 0 0 1258 1305 72 101 98 96 92 96 3509 2895 .984 1.017 .96 1.054 1.055 1.945 52 232 1.032 .93 80 5040 8490 27 35 318 326 0 1667 240 1427 .82 1384 1144 1.22 .774 -.286 -.369

Total number of rows: 37632

Table truncated, full table size 8537 Kbytes.




Supplementary data files not provided
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