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Sample GSM84850 Query DataSets for GSM84850
Status Public on Nov 23, 2005
Title p975-s2943 PBMC (VS)
Sample type RNA
 
Channel 1
Source name CRF, 1 round of amplification, Addie's from 3/01 and Kate's from 7/00, combined
Organism Homo sapiens
Characteristics CRF, 1 round of amplification, Addie's from 3/01 and Kate's from 7/00, combined
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name p975-s2943 PBMC (VS)
Organism Homo sapiens
Characteristics p975-s2943 PBMC (VS)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16827.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 GPL3120
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
1 500 660 108 232 392 428 491 656 110 238 383 424 0 0 114 144 21 57 100 100 100 100 820 807 .916 1.092 1.107 1.079 1.091 1.306 120 543 1.115 .93 120 2100 9020 110 122 78 90 0 545 192 354 .902 542 350 1.108 .915 -.148 -.128
2 571 986 109 242 462 744 563 1006 111 247 454 764 0 0 178 276 21 60 100 100 99 100 1206 1218 .621 1.61 1.683 1.607 1.622 1.302 120 401 1.606 .96 120 2250 9020 110 122 93 105 0 815 200 615 1.331 831 631 .751 1.391 .412 .476
3 3174 2077 111 247 3063 1830 3121 2004 133 256 3010 1757 0 0 839 581 90 70 100 100 100 100 4893 4767 1.674 .597 .584 .589 .585 1.146 120 412 .602 .99 130 2420 9020 109 122 109 122 0 1717 204 1512 .494 1656 1452 2.025 .482 -1.018 -1.052
4 2183 3160 113 257 2070 2903 2413 3421 135 264 2300 3164 0 0 1028 1560 92 68 97 99 96 98 4973 5464 .713 1.402 1.376 1.411 1.377 1.348 156 489 1.448 .99 140 2570 9020 109 123 124 138 0 2612 212 2399 1.159 2827 2615 .863 1.137 .213 .185
5 7872 4916 115 255 7757 4661 7696 4816 134 263 7581 4561 0 0 2064 1320 68 61 100 100 100 100 12418 12142 1.664 .601 .602 .598 .599 1.119 120 434 .6 .99 130 2730 9020 109 122 140 153 0 4063 211 3852 .497 3980 3769 2.014 .497 -1.01 -1.008
6 120 262 116 255 4 7 110 256 151 266 -6 1 0 0 34 68 120 67 1 15 0 2 11 -5 .571 1.75 null 1.692 1.705 3.16 80 423 3.641 .41 110 2860 9000 108 119 154 165 -50 217 211 6 1.446 212 1 .691 null .532 null
7 7885 2860 119 256 7766 2604 8029 3149 183 274 7910 2893 0 0 3824 1245 169 82 100 100 100 100 10370 10803 2.982 .335 .366 .336 .334 1.163 120 518 .33 .99 130 3050 9020 109 122 172 185 0 2364 212 2152 .277 2602 2391 3.609 .302 -1.851 -1.726
8 113 252 119 258 -6 -6 112 251 165 273 -7 -7 0 0 24 54 137 74 0 7 0 1 -12 -14 null null null 1.289 1.593 4.362 80 385 .426 .59 110 3180 9000 108 119 186 197 -50 208 213 -5 null 207 null null null null null
9 965 1217 118 256 847 961 1004 1260 124 267 886 1004 0 0 205 268 39 70 100 100 100 100 1808 1890 .881 1.135 1.133 1.114 1.136 1.189 80 361 1.135 .97 100 3350 9020 111 121 204 214 0 1006 212 794 .938 1041 830 1.066 .937 -.093 -.095
10 1174 1417 115 258 1059 1159 1285 1467 120 268 1170 1209 0 0 326 363 36 64 100 100 100 100 2218 2379 .914 1.094 1.033 1.097 1.102 1.152 120 450 1.092 .98 120 3510 9010 109 121 219 231 0 1171 213 958 .904 1212 999 1.106 .854 -.145 -.228
11 959 8275 116 272 843 8003 931 7952 120 282 815 7680 0 0 354 3197 27 68 100 100 100 100 8846 8495 .105 9.493 9.423 9.615 9.495 1.173 120 432 9.423 .98 130 3670 9020 109 122 234 247 0 6839 225 6614 7.846 6572 6347 .127 7.788 2.972 2.961
12 977 2890 125 294 852 2596 1013 3033 144 306 888 2739 0 0 248 792 57 84 100 100 99 100 3448 3627 .328 3.047 3.084 3.034 3.048 1.175 120 466 3.144 .98 120 3820 9010 109 121 250 262 0 2388 243 2145 2.518 2507 2264 .397 2.549 1.332 1.35
13 732 1130 127 288 605 842 636 1051 144 303 509 763 0 0 280 358 56 95 100 100 100 100 1447 1272 .719 1.392 1.499 1.411 1.419 1.222 80 404 1.39 .97 110 3990 9000 108 119 267 278 0 934 238 696 1.15 869 631 .869 1.239 .202 .309
14 1018 2276 123 284 895 1992 1033 2425 146 296 910 2141 0 0 278 603 82 86 100 100 98 100 2887 3051 .449 2.226 2.353 2.241 2.243 1.22 80 382 2.24 .97 110 4120 9010 109 120 280 291 0 1881 235 1646 1.839 2004 1769 .544 1.944 .879 .959
15 3560 1632 127 296 3433 1336 3384 1611 179 308 3257 1315 0 0 1585 586 126 87 100 100 100 100 4769 4572 2.57 .389 .404 .385 .374 1.238 120 499 .381 .97 120 4280 9010 109 121 296 308 0 1349 245 1104 .322 1331 1087 3.109 .334 -1.637 -1.583
16 809 901 143 330 666 571 780 891 182 342 637 561 0 0 149 153 109 101 100 100 100 100 1237 1198 1.166 .857 .881 .848 .836 1.223 52 310 .893 .93 90 4440 8990 108 117 313 322 0 745 273 472 .709 736 464 1.411 .728 -.497 -.458
17 1122 1021 141 329 981 692 1114 1009 166 346 973 680 0 0 121 139 76 100 100 100 100 100 1673 1653 1.418 .705 .699 .696 .705 1.257 52 294 .713 .94 90 4600 9010 110 119 329 338 0 844 272 572 .583 834 562 1.715 .578 -.778 -.792
18 2279 8383 121 314 2158 8069 2405 8863 145 332 2284 8549 0 0 664 2677 73 98 100 100 100 100 10227 10833 .267 3.739 3.743 3.718 3.737 1.151 120 483 3.83 .99 130 4750 9020 109 122 342 355 0 6928 260 6669 3.09 7325 7065 .324 3.093 1.628 1.629
19 1179 1261 121 318 1058 943 1208 1215 152 327 1087 897 0 0 300 370 92 86 100 100 100 100 2001 1984 1.122 .891 .825 .861 .85 1.229 120 407 .94 .95 120 4910 9020 110 122 359 371 0 1042 263 779 .737 1004 741 1.358 .682 -.441 -.552
20 2978 3885 137 329 2841 3556 3283 4319 175 341 3146 3990 0 0 1025 1391 94 97 100 100 100 100 6397 7136 .799 1.252 1.268 1.231 1.241 1.133 120 446 1.28 .99 120 5060 9020 110 122 374 386 0 3211 272 2939 1.034 3569 3298 .967 1.048 .049 .068

Total number of rows: 37632

Table truncated, full table size 8570 Kbytes.




Supplementary data files not provided
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