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Sample GSM84931 Query DataSets for GSM84931
Status Public on Nov 23, 2005
Title p878-s3603 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 p878-s3603 PBMC (VS)
Organism Homo sapiens
Characteristics p878-s3603 PBMC (VS)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/16800.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
1 819 1097 102 160 717 937 915 1172 105 166 813 1012 0 0 290 410 22 63 100 97 100 95 1654 1825 .765 1.307 1.245 1.245 1.304 1.499 120 604 1.352 .96 120 2240 8910 65 77 57 69 0 1192 174 1018 1.42 1274 1100 .704 1.353 .506 .436
2 1085 1653 105 162 980 1491 1081 1674 108 167 976 1512 0 0 169 323 23 62 100 100 100 100 2471 2488 .657 1.521 1.549 1.505 1.522 1.226 80 387 1.556 .97 110 2400 8910 65 76 73 84 0 1797 176 1621 1.654 1820 1643 .605 1.684 .726 .752
3 3124 2162 105 152 3019 2010 3225 2282 107 164 3120 2130 0 0 896 652 22 71 100 100 100 100 5029 5250 1.502 .666 .683 .663 .658 1.255 120 446 .66 .97 120 2550 8920 66 78 88 100 0 2350 165 2185 .724 2480 2315 1.382 .742 -.467 -.43
4 2336 3178 104 148 2232 3030 2493 3427 106 160 2389 3279 0 0 722 1147 22 70 100 100 100 99 5262 5668 .737 1.358 1.373 1.31 1.35 1.214 120 409 1.4 .98 120 2720 8920 66 78 105 117 0 3454 161 3293 1.476 3725 3564 .678 1.492 .561 .577
5 9801 7907 105 159 9696 7748 10732 8516 106 164 10627 8357 0 0 2815 2837 21 62 100 100 100 100 17444 18984 1.251 .799 .786 .776 .766 1.206 120 412 .82 .98 120 2870 8920 66 78 120 132 0 8595 173 8422 .869 9257 9084 1.151 .855 -.203 -.226
6 1462 3414 105 169 1357 3245 1452 3495 105 172 1347 3326 0 0 258 754 21 62 100 100 100 100 4602 4673 .418 2.391 2.469 2.362 2.386 1.202 80 369 2.441 .98 110 3030 8920 66 77 136 147 0 3711 184 3527 2.599 3799 3615 .385 2.684 1.378 1.424
7 8419 3025 102 163 8317 2862 8964 3291 107 166 8862 3128 0 0 3323 1208 43 61 100 100 100 100 11179 11990 2.906 .344 .353 .337 .34 1.229 120 435 .342 .98 120 3190 8920 66 78 152 164 0 3288 177 3111 .374 3577 3400 2.674 .384 -1.419 -1.382
8 1244 2448 102 163 1142 2285 1351 2591 106 169 1249 2428 0 0 414 817 44 67 100 100 100 100 3427 3677 .5 2.001 1.944 2.009 1.986 1.257 120 446 2.025 .97 120 3340 8920 66 78 167 179 0 2661 177 2484 2.175 2816 2639 .46 2.113 1.121 1.079
9 1985 3326 102 156 1883 3170 1985 3365 103 164 1883 3209 0 0 355 694 22 63 100 100 100 100 5053 5092 .594 1.683 1.704 1.672 1.68 1.133 80 396 1.697 .99 110 3500 8920 66 77 183 194 0 3615 170 3446 1.83 3658 3488 .546 1.852 .872 .889
10 1212 1749 102 157 1110 1592 1301 1767 103 161 1199 1610 0 0 388 566 20 60 100 100 100 100 2702 2809 .697 1.434 1.343 1.454 1.415 1.279 120 449 1.448 .97 120 3660 8920 66 78 199 211 0 1901 171 1730 1.559 1921 1750 .641 1.46 .641 .546
11 1260 10303 99 164 1161 10139 1416 11453 100 168 1317 11289 0 0 470 4287 20 61 100 100 100 100 11300 12606 .115 8.733 8.572 8.741 8.693 1.247 120 414 8.985 .98 120 3820 8920 66 78 215 227 0 11199 178 11021 9.492 12449 12271 .105 9.317 3.247 3.22
12 623 1528 98 166 525 1362 629 1553 99 171 531 1387 0 0 232 548 19 61 99 100 99 100 1887 1918 .385 2.594 2.612 2.72 2.582 1.384 120 403 2.594 .96 120 3970 8920 66 78 230 242 0 1661 180 1480 2.82 1688 1508 .355 2.839 1.496 1.505
13 1349 2256 98 168 1251 2088 1480 2340 100 173 1382 2172 0 0 452 760 19 63 100 100 100 100 3339 3554 .599 1.669 1.572 1.701 1.683 1.312 120 419 1.693 .97 120 4120 8920 66 78 245 257 0 2452 183 2270 1.814 2543 2361 .551 1.708 .859 .773
14 666 1259 98 169 568 1090 664 1285 99 173 566 1116 0 0 211 398 19 61 100 100 100 100 1658 1682 .521 1.919 1.972 1.93 1.888 1.281 80 377 1.956 .96 110 4270 8910 65 76 260 271 0 1368 184 1185 2.086 1397 1213 .479 2.143 1.061 1.1
15 4296 2544 100 169 4196 2375 4644 2688 102 173 4544 2519 0 0 1543 997 27 60 100 99 99 98 6571 7063 1.767 .566 .554 .547 .565 1.212 120 416 .574 .98 120 4430 8910 65 77 276 288 0 2765 184 2582 .615 2922 2738 1.625 .603 -.701 -.731
16 605 820 99 174 506 646 612 848 106 179 513 674 0 0 177 247 43 67 95 96 95 95 1152 1187 .783 1.277 1.314 1.292 1.296 1.479 120 409 1.34 .93 120 4580 8910 65 77 291 303 0 891 189 702 1.388 922 733 .721 1.428 .473 .514
17 460 524 100 175 360 349 479 511 109 184 379 336 0 0 155 195 47 83 95 93 92 87 709 715 1.032 .969 .887 .928 .953 1.868 120 409 1.101 .85 120 4740 8920 66 78 307 319 0 570 190 379 1.054 555 365 .949 .964 .076 -.053
18 931 2884 104 180 827 2704 977 2930 111 192 873 2750 0 0 257 880 50 91 99 99 97 99 3531 3623 .306 3.27 3.15 3.287 3.301 1.283 120 402 3.351 .97 120 4900 8920 66 78 323 335 0 3135 196 2939 3.554 3185 2989 .281 3.424 1.829 1.776
19 721 567 103 186 618 381 733 556 111 195 630 370 0 0 150 138 50 84 100 98 100 93 999 1000 1.622 .617 .587 .589 .599 1.522 80 339 .666 .85 110 5050 8920 66 77 338 349 0 616 202 414 .67 604 402 1.492 .638 -.578 -.648
20 1009 1758 105 177 904 1581 1064 1785 108 190 959 1608 0 0 263 458 32 75 99 100 99 99 2485 2567 .572 1.749 1.677 1.788 1.734 1.405 120 479 1.761 .97 120 5210 8920 66 78 354 366 0 1911 192 1718 1.901 1940 1748 .526 1.823 .927 .866

Total number of rows: 37632

Table truncated, full table size 8513 Kbytes.




Supplementary data files not provided
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