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Sample GSM84924 Query DataSets for GSM84924
Status Public on Nov 23, 2005
Title s6696, p327, 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 s6696, p327, Pax whole blood
Organism Homo sapiens
Characteristics s6696, p327, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23008.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 1584 3522 213 266 1371 3256 1594 3843 264 441 1381 3577 0 0 878 1821 540 1462 77 79 64 59 4627 4958 .421 2.375 2.59 2.617 2.323 1.689 120 549 2.506 .96 120 2130 8270 33 45 39 51 0 1834 139 1696 1.237 2002 1863 .808 1.349 .307 .432
2 2500 7222 225 278 2275 6944 2619 7494 285 498 2394 7216 0 0 853 2079 632 1706 96 100 88 92 9219 9610 .328 3.052 3.014 3.303 3.054 1.651 80 398 3.104 .94 110 2280 8280 34 45 54 65 0 3761 145 3617 1.59 3903 3758 .629 1.57 .669 .651
3 1880 15073 223 254 1657 14819 1964 16581 228 267 1741 16327 0 0 805 5329 60 93 100 100 97 100 16476 18068 .112 8.943 9.378 9.967 9.212 1.614 80 465 8.635 .96 110 2450 8270 33 44 71 82 0 7851 132 7718 4.658 8636 8504 .215 4.884 2.22 2.288
4 1978 4833 223 239 1755 4594 2064 4826 226 243 1841 4587 0 0 631 1444 47 67 98 100 98 100 6349 6428 .382 2.618 2.492 2.736 2.634 1.448 80 366 2.624 .96 100 2600 8280 35 45 87 97 0 2517 124 2393 1.363 2514 2389 .733 1.298 .447 .376
5 1110 1794 218 235 892 1559 1083 1645 219 239 865 1410 0 0 414 674 46 64 98 100 98 100 2451 2275 .572 1.748 1.63 1.852 1.738 1.593 80 417 1.905 .89 110 2750 8280 34 45 101 112 0 934 122 812 .91 857 734 1.099 .849 -.136 -.236
6 1549 7023 211 231 1338 6792 1585 7523 216 233 1374 7292 0 0 646 2134 43 70 98 100 96 100 8130 8666 .197 5.076 5.307 5.754 5.04 1.746 80 379 4.831 .95 100 2920 8270 34 44 119 129 0 3658 120 3538 2.644 3918 3798 .378 2.764 1.403 1.467
7 2448 6337 212 227 2236 6110 2542 6794 217 229 2330 6567 0 0 840 1522 44 67 98 100 98 100 8346 8897 .366 2.733 2.818 2.885 2.665 1.36 80 437 2.671 .96 110 3080 8270 33 44 134 145 0 3301 118 3182 1.423 3539 3420 .703 1.468 .509 .554
8 1628 3144 215 232 1413 2912 1595 3141 220 238 1380 2909 0 0 357 592 45 66 100 100 100 100 4325 4289 .485 2.061 2.108 2.084 2.068 1.195 80 404 2.062 .96 110 3240 8280 34 45 150 161 0 1638 121 1517 1.073 1636 1515 .932 1.098 .102 .135
9 2265 3391 211 232 2054 3159 2396 3307 220 245 2185 3075 0 0 720 969 69 135 100 100 100 100 5213 5260 .65 1.538 1.407 1.598 1.427 1.415 80 427 1.581 .94 110 3390 8270 33 44 165 176 0 1766 121 1645 .801 1722 1602 1.248 .733 -.32 -.448
10 1884 3474 212 235 1672 3239 1907 3391 235 287 1695 3156 0 0 614 833 182 377 100 100 100 100 4911 4851 .516 1.937 1.862 2.02 1.94 1.312 80 390 1.893 .95 100 3550 8270 34 44 182 192 0 1809 122 1687 1.009 1766 1644 .991 .97 .013 -.044
11 2170 4000 212 224 1958 3776 2225 3960 221 230 2013 3736 0 0 625 842 51 67 100 100 98 100 5734 5749 .519 1.928 1.856 2.032 1.943 1.396 80 423 1.934 .94 110 3700 8270 33 44 196 207 0 2083 117 1967 1.004 2063 1946 .996 .967 .006 -.049
12 1434 2731 214 224 1220 2507 1067 2638 223 231 853 2414 0 0 1267 1794 58 65 81 92 80 91 3727 3267 .487 2.055 2.83 2.19 1.986 2.253 80 354 1.75 .93 100 3860 8280 35 45 213 223 0 1422 117 1306 1.07 1374 1257 .934 1.474 .098 .56
13 1510 2623 215 228 1295 2395 1568 2706 221 234 1353 2478 0 0 379 439 55 66 100 100 100 100 3690 3831 .541 1.849 1.831 1.933 1.814 1.367 80 380 1.842 .95 100 4020 8270 34 44 229 239 0 1366 119 1247 .963 1409 1291 1.038 .954 -.054 -.068
14 4866 5305 221 248 4645 5057 5101 5650 226 252 4880 5402 0 0 1772 1389 55 69 100 100 100 100 9702 10282 .919 1.089 1.107 1.142 1.043 1.356 80 421 1.037 .95 110 4180 8270 33 44 244 255 0 2763 129 2634 .567 2943 2814 1.764 .577 -.819 -.794
15 1687 3120 216 257 1471 2863 1736 3162 221 263 1520 2905 0 0 482 498 52 73 100 100 100 100 4334 4425 .514 1.946 1.911 2.051 1.927 1.4 80 365 1.951 .92 100 4340 8270 34 44 261 271 0 1625 134 1491 1.014 1647 1513 .986 .995 .02 -.007
16 2650 17661 222 267 2428 17394 2737 18627 224 288 2515 18360 0 0 898 4318 48 120 98 100 98 100 19822 20875 .14 7.164 7.3 7.589 7.121 1.516 80 402 7.078 .95 110 4490 8270 33 44 275 286 0 9198 139 9059 3.731 9702 9563 .268 3.802 1.9 1.927
17 2950 2644 213 255 2737 2389 2935 2649 219 266 2722 2394 0 0 992 843 47 95 100 100 100 100 5126 5116 1.146 .873 .88 .886 .876 1.383 80 402 .888 .9 110 4640 8270 33 44 290 301 0 1377 133 1244 .455 1380 1247 2.2 .458 -1.137 -1.126
18 1631 2681 211 264 1420 2417 1708 2750 240 272 1497 2486 0 0 548 677 450 75 96 100 82 100 3837 3983 .588 1.702 1.661 1.811 1.72 1.432 80 430 1.726 .94 110 4800 8270 33 44 306 317 0 1396 138 1259 .887 1432 1295 1.128 .865 -.174 -.209
19 469 534 219 278 250 256 250 271 223 282 31 -7 0 0 493 677 54 68 42 31 33 28 506 24 .977 1.024 null 1.381 1.649 4.728 80 366 1.387 .89 100 4960 8270 34 44 323 333 -50 278 145 133 .533 141 null 1.875 null -.907 null
20 2000 2580 231 284 1769 2296 2154 2418 236 294 1923 2134 0 0 914 1226 52 77 100 100 100 100 4065 4057 .77 1.298 1.11 1.348 1.195 1.573 52 256 1.349 .91 80 5110 8270 35 43 339 347 0 1344 148 1196 .676 1259 1111 1.479 .578 -.565 -.791

Total number of rows: 37632

Table truncated, full table size 8807 Kbytes.




Supplementary data files not provided
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