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Sample GSM84830 Query DataSets for GSM84830
Status Public on Nov 23, 2005
Title p618-s3937 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 p618-s3937 PBMC (VS), amplified on 4/23/01
Organism Homo sapiens
Characteristics p618-s3937 PBMC (VS), amplified on 4/23/01
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, PBMC
Image: http://smd.stanford.edu/MicroArray/gifs/2001-05/17194.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
1 451 408 69 124 382 284 391 375 72 126 322 251 0 0 174 153 20 40 100 99 100 96 666 573 1.345 .743 .78 .695 .741 1.544 120 652 .777 .93 130 2140 8620 39 52 79 92 0 628 191 437 1.144 577 386 .874 1.199 .194 .262
2 549 521 70 128 479 393 455 438 76 133 385 310 0 0 262 256 29 42 99 100 99 97 872 695 1.219 .82 .805 .781 .76 1.568 120 473 .871 .94 130 2300 8620 39 52 95 108 0 802 197 605 1.262 674 477 .792 1.239 .336 .309
3 2371 923 70 128 2301 795 2119 833 75 132 2049 705 0 0 843 329 26 40 100 100 100 100 3096 2754 2.894 .346 .344 .34 .338 1.221 120 456 .337 .96 130 2460 8620 39 52 111 124 0 1420 197 1223 .532 1282 1085 1.881 .529 -.912 -.918
4 2320 2137 70 127 2250 2010 2159 1967 82 131 2089 1840 0 0 1108 1025 60 44 100 100 100 100 4260 3929 1.119 .893 .881 .872 .861 1.191 120 408 .897 .98 130 2620 8630 40 53 127 140 0 3288 195 3092 1.374 3026 2831 .728 1.355 .459 .438
5 6023 2565 72 122 5951 2443 5701 2427 84 127 5629 2305 0 0 2009 907 59 44 100 100 100 100 8394 7934 2.436 .411 .409 .409 .41 1.169 120 457 .408 .98 130 2780 8620 39 52 143 156 0 3946 188 3758 .632 3734 3546 1.583 .63 -.663 -.667
6 88 146 81 134 7 12 77 131 200 159 -4 -3 0 0 50 55 262 89 1 10 0 1 19 -7 .583 1.714 null 2.187 2 3.159 80 395 .3 .77 110 2930 8610 39 50 159 170 -50 225 206 18 2.637 202 null .379 null 1.399 null
7 10146 2570 86 136 10060 2434 8610 2210 190 172 8524 2074 0 0 5720 1601 238 309 100 98 100 91 12494 10598 4.133 .242 .243 .233 .224 1.229 120 515 .247 .96 130 3110 8620 39 52 176 189 0 3954 209 3745 .372 3400 3191 2.687 .374 -1.426 -1.418
8 75 153 77 125 -2 28 72 151 92 154 -5 26 0 0 18 49 59 347 2 0 0 0 26 21 null null null 2.748 1.877 3.807 80 388 31.509 .39 110 3240 8610 39 50 190 201 -50 235 192 43 null 232 40 null null null null
9 1645 2259 81 143 1564 2116 1568 2046 107 176 1487 1903 0 0 665 1218 69 105 100 100 100 97 3680 3390 .739 1.353 1.28 1.24 1.31 1.313 80 435 1.452 .97 110 3410 8620 40 51 207 218 0 3475 220 3255 2.081 3148 2928 .48 1.969 1.058 .977
10 824 808 80 154 744 654 870 790 114 194 790 636 0 0 295 342 82 125 100 98 100 87 1398 1426 1.138 .879 .805 .821 .866 1.318 120 457 .948 .95 120 3580 8620 40 52 224 236 0 1243 237 1006 1.352 1215 978 .739 1.239 .435 .309
11 641 4860 73 142 568 4718 572 4549 94 178 499 4407 0 0 247 2021 65 131 100 100 100 100 5286 4906 .12 8.306 8.832 8.326 8.148 1.211 120 436 8.424 .97 130 3740 8620 39 52 239 252 0 7477 218 7258 12.779 6998 6780 .078 13.587 3.676 3.764
12 763 1327 74 142 689 1185 774 1338 91 183 700 1196 0 0 238 444 55 143 100 100 100 99 1874 1896 .581 1.72 1.709 1.696 1.709 1.197 120 410 1.739 .97 120 3890 8620 40 52 255 267 0 2042 218 1823 2.646 2058 1840 .378 2.629 1.404 1.394
13 1084 2027 74 140 1010 1887 759 1428 88 159 685 1288 0 0 765 1422 48 100 100 100 100 100 2897 1973 .535 1.868 1.88 1.889 1.877 1.297 120 454 1.887 .98 120 4050 8620 40 52 271 283 0 3118 215 2903 2.874 2197 1982 .348 2.893 1.523 1.532
14 1308 1113 70 128 1238 985 1136 1213 82 135 1066 1085 0 0 738 575 57 47 100 99 99 95 2223 2151 1.257 .796 1.018 .684 .842 2.215 120 457 .765 .84 130 4220 8610 38 51 287 300 -100 1712 197 1515 1.224 1866 1669 .817 1.566 .292 .647
15 4703 1707 71 124 4632 1583 4810 1710 135 138 4739 1586 0 0 2456 944 430 88 98 99 94 94 6215 6325 2.926 .342 .335 .322 .339 1.332 156 552 .346 .97 150 4360 8610 37 52 300 315 -100 2626 191 2435 .526 2631 2440 1.902 .515 -.927 -.958
16 2035 952 71 117 1964 835 1390 764 137 132 1319 647 0 0 1686 645 447 89 86 92 67 88 2799 1966 2.352 .425 .491 .44 .546 1.918 156 505 .319 .81 140 4520 8590 36 50 317 331 -100 1465 180 1285 .654 1175 995 1.529 .755 -.612 -.406
17 1131 713 70 117 1061 596 1017 589 75 122 947 472 0 0 959 546 32 38 89 91 85 86 1657 1419 1.78 .562 .498 .617 .579 2.168 156 490 .528 .9 140 4670 8610 38 52 332 346 -100 1097 180 917 .864 906 726 1.157 .767 -.211 -.383
18 2397 5346 70 121 2327 5225 2610 5472 76 129 2540 5351 0 0 741 1927 31 49 100 100 100 100 7552 7891 .445 2.245 2.107 2.22 2.19 1.167 120 369 2.326 .98 130 4830 8630 40 53 348 361 0 8225 186 8038 3.454 8418 8232 .289 3.241 1.788 1.696
19 1844 1420 71 120 1773 1300 1766 1147 94 135 1695 1027 0 0 785 814 99 68 100 100 100 100 3073 2722 1.364 .733 .606 .676 .667 1.328 120 403 .803 .95 130 4990 8630 40 53 364 377 0 2185 185 2000 1.128 1765 1580 .887 .932 .174 -.101
20 2826 2245 75 131 2751 2114 3104 2291 114 144 3029 2160 0 0 1041 975 130 73 100 100 100 100 4865 5189 1.301 .768 .713 .749 .731 1.202 120 446 .798 .97 130 5140 8630 40 53 379 392 0 3454 202 3252 1.182 3525 3323 .846 1.097 .242 .134

Total number of rows: 37632

Table truncated, full table size 8304 Kbytes.




Supplementary data files not provided
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