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Sample GSM84951 Query DataSets for GSM84951
Status Public on Nov 23, 2005
Title s7205, p878, 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 s7205, p878, Pax whole blood
Organism Homo sapiens
Characteristics s7205, p878, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23095.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 1094 2114 249 355 845 1759 1059 1877 252 363 810 1522 0 0 689 1278 54 103 88 92 82 90 2604 2332 .48 2.082 1.879 2.121 2.008 1.753 80 503 2.077 .93 110 1920 8550 25 36 37 48 0 1888 317 1571 1.859 1676 1359 .538 1.678 .894 .746
2 1401 4029 238 346 1163 3683 1302 3266 245 359 1064 2920 0 0 1130 3124 60 109 75 90 73 85 4846 3984 .316 3.167 2.744 3.221 2.968 1.681 80 392 3.022 .96 100 2070 8550 26 36 53 63 0 3597 309 3288 2.828 2916 2607 .354 2.45 1.5 1.293
3 1500 6620 218 328 1282 6292 1375 6208 220 345 1157 5880 0 0 651 2990 49 109 96 100 96 100 7574 7037 .204 4.908 5.082 5.075 4.834 1.392 80 449 4.864 .97 110 2230 8550 25 36 68 79 0 5911 293 5618 4.382 5543 5250 .228 4.538 2.132 2.182
4 1038 2664 201 320 837 2344 797 2220 212 352 596 1900 0 0 986 2335 93 222 63 76 62 68 3181 2496 .357 2.8 3.188 2.491 2.6 2.071 80 435 2.558 .96 110 2390 8550 25 36 84 95 0 2379 286 2093 2.5 1982 1696 .4 2.846 1.322 1.509
5 880 2193 200 299 680 1894 835 2020 219 345 635 1721 0 0 661 1571 122 282 75 80 69 78 2574 2356 .359 2.785 2.71 2.53 2.657 2.314 52 251 2.77 .94 90 2550 8560 27 36 101 110 0 1958 267 1691 2.487 1804 1537 .402 2.42 1.314 1.275
6 1147 4248 191 299 956 3949 792 3191 197 320 601 2892 0 0 1199 4060 56 175 63 77 57 73 4905 3493 .242 4.131 4.812 3.764 4.071 2.451 80 376 3.81 .95 110 2690 8540 24 35 114 125 0 3793 267 3526 3.688 2849 2582 .271 4.296 1.883 2.103
7 1768 4655 187 300 1581 4355 1733 4508 192 317 1546 4208 0 0 1267 3463 44 179 87 90 82 83 5936 5754 .363 2.755 2.722 2.843 2.701 1.941 80 347 2.763 .96 110 2850 8540 24 35 130 141 0 4156 268 3888 2.459 4025 3757 .407 2.43 1.298 1.281
8 1504 3970 193 298 1311 3672 1414 3387 207 335 1221 3089 0 0 992 2791 118 336 88 90 81 84 4983 4310 .357 2.801 2.53 2.843 2.719 2.013 120 439 2.878 .96 120 3000 8540 24 36 145 157 0 3545 266 3279 2.501 3024 2758 .4 2.259 1.322 1.176
9 2033 4444 189 300 1844 4144 1984 4245 209 345 1795 3945 0 0 1310 2770 132 357 85 87 82 85 5988 5740 .445 2.247 2.198 2.452 2.329 1.528 80 415 2.195 .97 110 3160 8530 23 34 161 172 0 3968 268 3700 2.007 3790 3522 .498 1.962 1.005 .973
10 1320 2841 195 300 1125 2541 1015 1860 222 355 820 1560 0 0 1379 2973 161 321 66 72 61 66 3666 2380 .443 2.259 1.902 2.164 2.083 2.334 80 337 2.196 .97 100 3320 8530 24 34 178 188 0 2537 268 2269 2.017 1661 1393 .496 1.699 1.012 .764
11 1341 3172 195 302 1146 2870 1118 2821 241 414 923 2519 0 0 1161 2443 255 563 66 78 60 72 4016 3442 .399 2.504 2.729 2.549 2.261 2.272 80 444 2.343 .94 110 3470 8520 22 33 192 203 0 2832 270 2563 2.236 2519 2249 .447 2.437 1.161 1.285
12 1010 2097 187 293 823 1804 700 1560 209 342 513 1267 0 0 924 1875 189 407 60 67 56 58 2627 1780 .456 2.192 2.47 2.29 2.014 2.908 80 330 2.175 .94 100 3640 8540 25 35 210 220 0 1872 262 1611 1.957 1393 1131 .511 2.205 .969 1.141
13 886 3084 184 274 702 2810 825 2728 244 327 641 2454 0 0 671 2325 455 282 61 85 34 80 3512 3095 .25 4.003 3.828 3.791 3.723 1.928 120 466 3.89 .94 120 3790 8540 24 36 224 236 0 2754 245 2509 3.574 2436 2191 .28 3.418 1.838 1.773
14 2744 2902 176 267 2568 2635 2572 2695 283 346 2396 2428 0 0 2149 2100 621 423 71 80 67 72 5203 4824 .975 1.026 1.013 1.012 .979 1.548 80 412 .941 .95 110 3950 8510 21 32 240 251 0 2591 238 2353 .916 2406 2168 1.092 .905 -.126 -.144
15 976 1892 176 259 800 1633 945 1821 239 315 769 1562 0 0 605 1204 446 377 67 81 37 71 2433 2331 .49 2.041 2.031 1.981 1.92 1.764 80 331 2.068 .96 100 4110 8530 24 34 257 267 0 1689 231 1458 1.823 1626 1395 .549 1.814 .866 .859
16 1869 6139 176 259 1693 5880 1942 6451 179 265 1766 6192 0 0 912 2875 38 86 95 100 95 100 7573 7958 .288 3.473 3.506 3.882 3.458 1.78 120 451 3.442 .97 120 4260 8530 23 35 271 283 0 5481 231 5250 3.101 5760 5529 .322 3.131 1.633 1.646
17 1545 1429 174 258 1371 1171 1642 1500 178 264 1468 1242 0 0 833 693 38 81 91 91 87 90 2542 2710 1.171 .854 .846 .852 .851 2.201 80 412 .836 .94 110 4420 8530 23 34 287 298 0 1276 230 1046 .763 1339 1109 1.311 .755 -.391 -.405
18 1202 2670 174 267 1028 2403 1270 2735 191 299 1096 2468 0 0 647 1312 121 217 87 97 85 93 3431 3564 .428 2.338 2.252 2.683 2.355 1.942 80 371 2.275 .95 100 4580 8540 25 35 304 314 0 2384 238 2146 2.087 2442 2204 .479 2.011 1.061 1.008
19 389 425 173 270 216 155 245 308 180 272 72 38 0 0 363 296 43 78 57 38 43 31 371 110 1.394 .718 .528 1.095 .934 3.258 80 365 .846 .73 100 4740 8540 25 35 320 330 -50 379 241 138 .641 275 34 1.561 .471 -.642 -1.085
20 1129 1081 176 266 953 815 1062 1114 190 285 886 848 0 0 634 526 96 173 90 84 90 75 1768 1734 1.169 .855 .957 .815 .835 1.861 52 315 .86 .93 90 4900 8530 24 33 336 345 0 965 238 728 .764 995 757 1.31 .855 -.389 -.227

Total number of rows: 37632

Table truncated, full table size 8485 Kbytes.




Supplementary data files not provided
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