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Sample GSM84918 Query DataSets for GSM84918
Status Public on Nov 23, 2005
Title s5768, p149, 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 s5768, p149, Pax whole blood
Organism Homo sapiens
Characteristics s5768, p149, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22927.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
1 914 1428 114 289 800 1139 901 1400 117 295 787 1111 0 0 310 498 20 102 100 100 100 100 1939 1898 .702 1.424 1.412 1.403 1.407 1.318 80 401 1.498 .95 100 2330 8470 42 52 53 63 0 1720 348 1372 1.715 1687 1339 .583 1.701 .779 .766
2 889 1498 116 280 773 1218 881 1483 118 293 765 1203 0 0 254 386 20 101 100 100 100 100 1991 1968 .635 1.576 1.573 1.572 1.543 1.34 80 380 1.609 .94 100 2490 8480 43 53 69 79 0 1805 337 1467 1.898 1787 1449 .527 1.895 .925 .922
3 662 1595 115 285 547 1310 679 1580 117 297 564 1295 0 0 221 498 19 107 100 100 100 100 1857 1859 .418 2.395 2.296 2.442 2.389 1.368 80 385 2.486 .94 100 2640 8470 42 52 84 94 0 1922 343 1578 2.885 1904 1560 .347 2.766 1.529 1.468
4 947 1481 113 274 834 1207 966 1514 114 279 853 1240 0 0 325 516 22 105 100 96 100 96 2041 2093 .691 1.447 1.454 1.373 1.439 1.476 80 486 1.516 .94 110 2800 8470 41 52 99 110 0 1784 330 1454 1.744 1824 1494 .574 1.751 .802 .809
5 417 727 110 264 307 463 413 730 112 275 303 466 0 0 91 194 20 97 100 97 100 93 770 769 .663 1.508 1.538 1.361 1.54 2.034 80 403 1.846 .83 100 2960 8480 43 53 116 126 0 876 318 558 1.817 880 561 .55 1.853 .862 .89
6 976 2315 110 265 866 2050 967 2370 112 278 857 2105 0 0 254 558 19 101 100 100 100 100 2916 2962 .422 2.367 2.456 2.391 2.452 1.257 80 386 2.383 .96 100 3130 8480 43 53 133 143 0 2789 319 2470 2.852 2855 2536 .351 2.959 1.512 1.565
7 1928 2941 108 256 1820 2685 1891 2960 110 273 1783 2704 0 0 587 903 18 103 100 100 100 100 4505 4487 .678 1.475 1.517 1.475 1.479 1.217 80 428 1.497 .97 110 3280 8470 41 52 147 158 0 3543 308 3235 1.777 3566 3258 .563 1.827 .83 .87
8 830 1306 109 277 721 1029 824 1312 111 282 715 1035 0 0 169 312 23 107 100 100 100 100 1750 1750 .701 1.427 1.448 1.402 1.382 1.36 80 384 1.526 .93 100 3440 8480 43 53 164 174 0 1573 334 1240 1.719 1581 1247 .582 1.744 .782 .802
9 1711 1906 110 280 1601 1626 1712 1837 111 287 1602 1557 0 0 524 527 19 103 100 100 100 100 3227 3159 .985 1.016 .972 1.025 1.008 1.274 80 364 1.011 .96 100 3580 8450 40 50 178 188 0 2296 337 1959 1.224 2213 1876 .817 1.171 .291 .228
10 2210 3305 111 288 2099 3017 1931 2796 113 288 1820 2508 0 0 1232 1769 20 100 100 100 100 100 5116 4328 .696 1.437 1.378 1.458 1.445 1.281 80 441 1.447 .98 110 3740 8470 41 52 193 204 0 3982 347 3635 1.732 3369 3022 .577 1.66 .792 .731
11 1656 2486 107 266 1549 2220 1670 2356 109 275 1563 2090 0 0 524 787 19 102 100 100 100 100 3769 3653 .698 1.433 1.337 1.433 1.419 1.226 80 431 1.457 .97 110 3900 8460 40 51 209 220 0 2995 320 2675 1.727 2839 2518 .579 1.611 .788 .688
12 2196 3413 106 270 2090 3143 2211 3257 107 277 2105 2987 0 0 975 1613 17 108 100 100 100 100 5233 5092 .665 1.504 1.419 1.47 1.445 1.263 80 421 1.546 .98 110 4060 8470 41 52 225 236 0 4112 325 3787 1.812 3924 3599 .552 1.71 .857 .774
13 1390 1941 109 268 1281 1673 1357 1863 110 274 1248 1595 0 0 524 662 19 104 100 100 100 100 2954 2843 .766 1.306 1.278 1.318 1.281 1.33 80 419 1.31 .95 110 4210 8460 40 51 240 251 0 2339 323 2016 1.574 2245 1922 .636 1.54 .654 .623
14 4240 4760 110 270 4130 4490 4428 4908 112 275 4318 4638 0 0 1792 1921 19 101 100 100 100 100 8620 8956 .92 1.087 1.074 1.107 1.086 1.217 80 365 1.076 .99 100 4370 8460 41 51 257 267 0 5735 325 5410 1.31 5913 5588 .763 1.294 .389 .372
15 2070 3276 106 276 1964 3000 1863 3224 107 282 1757 2948 0 0 969 1398 18 98 100 100 100 100 4964 4705 .655 1.527 1.678 1.553 1.52 1.28 80 391 1.526 .98 100 4530 8460 41 51 273 283 0 3947 333 3614 1.84 3884 3552 .543 2.022 .88 1.015
16 1347 5079 102 260 1245 4819 1391 4975 102 268 1289 4715 0 0 385 1176 18 103 100 100 100 100 6064 6004 .258 3.871 3.658 3.984 3.789 1.263 80 433 3.853 .98 110 4700 8460 40 51 289 300 0 6119 313 5806 4.663 5994 5681 .214 4.407 2.221 2.14
17 1183 760 100 243 1083 517 1128 713 101 254 1028 470 0 0 337 233 16 92 100 97 100 93 1600 1498 2.095 .477 .457 .438 .492 1.731 80 392 .486 .87 100 4850 8460 41 51 305 315 0 916 293 623 .575 859 566 1.739 .551 -.798 -.86
18 778 1607 102 255 676 1352 835 1666 103 263 733 1411 0 0 264 501 17 96 100 100 100 100 2028 2144 .5 2 1.925 2.024 1.993 1.292 80 387 2.06 .95 100 5020 8470 42 52 322 332 0 1936 307 1629 2.41 2007 1700 .415 2.319 1.269 1.214
19 219 320 102 249 117 71 138 300 103 262 36 51 0 0 210 165 18 101 75 36 48 17 188 87 1.648 .607 1.417 1.617 1.542 3.973 80 368 .955 .6 100 5170 8460 41 51 337 347 -50 386 300 86 .731 361 61 1.368 1.707 -.452 .771
20 967 753 102 248 865 505 918 686 103 253 816 438 0 0 445 266 18 96 100 100 100 90 1370 1254 1.713 .584 .537 .581 .588 1.508 52 314 .574 .88 90 5320 8460 41 50 352 361 0 907 299 608 .703 827 528 1.422 .647 -.508 -.629

Total number of rows: 37632

Table truncated, full table size 8600 Kbytes.




Supplementary data files not provided
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