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Sample GSM84882 Query DataSets for GSM84882
Status Public on Nov 23, 2005
Title s5087, p457, 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 s5087, p457, Pax whole blood
Organism Homo sapiens
Characteristics s5087, p457, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23121.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
1 495 889 77 125 418 764 523 890 79 139 446 765 0 0 149 278 17 60 100 100 100 100 1182 1211 .547 1.828 1.715 1.829 1.772 1.39 80 423 1.942 .92 100 1890 8130 37 47 34 44 0 863 121 742 1.775 864 743 .564 1.665 .827 .736
2 638 1431 78 131 560 1300 678 1478 82 144 600 1347 0 0 314 585 25 68 98 100 95 100 1860 1947 .431 2.321 2.245 2.594 2.307 1.651 80 445 2.286 .93 110 2040 8140 37 48 48 59 0 1389 127 1262 2.254 1435 1308 .444 2.18 1.172 1.124
3 662 1817 78 127 584 1690 693 1930 80 137 615 1803 0 0 197 511 16 60 100 100 100 100 2274 2418 .346 2.894 2.932 2.943 2.929 1.3 80 438 3.049 .96 110 2200 8120 35 46 64 75 0 1764 123 1641 2.81 1874 1750 .356 2.846 1.49 1.509
4 633 1251 78 124 555 1127 651 1188 80 134 573 1064 0 0 239 509 20 62 100 100 98 100 1682 1637 .492 2.031 1.857 2.079 1.931 1.526 80 378 2.184 .93 100 2360 8120 36 46 81 91 0 1215 120 1094 1.971 1153 1033 .507 1.803 .979 .85
5 376 682 81 127 295 555 382 657 89 154 301 530 0 0 123 235 43 98 98 100 94 100 850 831 .532 1.881 1.761 1.955 1.6 1.821 52 343 2.076 .85 90 2520 8110 35 44 97 106 0 662 123 539 1.827 638 515 .547 1.71 .869 .774
6 494 1699 77 127 417 1572 491 1706 79 137 414 1579 0 0 181 551 19 60 98 100 97 100 1989 1993 .265 3.77 3.814 3.907 3.868 1.359 80 380 3.846 .94 100 2680 8130 37 47 113 123 0 1650 123 1526 3.66 1656 1533 .273 3.703 1.872 1.889
7 1039 1945 78 127 961 1818 989 1984 80 140 911 1857 0 0 558 843 22 69 97 100 96 98 2779 2768 .529 1.892 2.038 2.26 1.888 1.988 80 352 1.841 .94 100 2840 8120 36 46 129 139 0 1888 123 1765 1.837 1926 1803 .544 1.979 .877 .985
8 654 1177 76 129 578 1048 672 1137 78 139 596 1008 0 0 168 384 20 67 100 98 100 98 1626 1604 .552 1.813 1.691 1.775 1.744 1.353 80 367 1.919 .94 100 2990 8120 36 46 144 154 0 1143 125 1017 1.76 1104 979 .568 1.642 .816 .715
9 1344 1768 75 137 1269 1631 1411 2004 78 157 1336 1867 0 0 944 1087 31 151 88 85 81 78 2900 3203 .778 1.285 1.397 1.525 1.295 2.488 80 420 1.217 .94 110 3150 8110 34 45 159 170 0 1717 133 1583 1.248 1946 1813 .801 1.357 .319 .44
10 916 1662 74 136 842 1526 894 1546 78 159 820 1410 0 0 634 1045 33 166 96 90 86 85 2368 2230 .552 1.812 1.72 2.033 1.755 1.723 80 333 1.792 .94 100 3310 8110 35 45 176 186 0 1614 132 1482 1.76 1501 1369 .568 1.669 .815 .739
11 820 1765 77 129 743 1636 650 1674 81 149 573 1545 0 0 687 1378 31 119 82 86 73 75 2379 2118 .454 2.202 2.696 2.353 2.103 1.933 80 409 2.137 .94 110 3450 8110 34 45 189 200 0 1714 125 1588 2.138 1625 1500 .468 2.618 1.096 1.388
12 721 1603 75 130 646 1473 566 1234 79 145 491 1104 0 0 634 1396 29 94 80 85 76 80 2119 1595 .439 2.28 2.248 2.47 2.2 1.862 80 379 2.301 .95 100 3620 8110 35 45 207 217 0 1556 126 1430 2.214 1198 1072 .452 2.183 1.147 1.126
13 1081 2745 73 134 1008 2611 1060 2614 105 139 987 2480 0 0 770 2081 416 60 68 95 58 91 3619 3467 .386 2.59 2.513 3.065 2.74 2.018 80 419 2.726 .95 110 3770 8120 35 46 221 232 0 2665 130 2535 2.515 2538 2408 .398 2.439 1.33 1.287
14 2324 3132 74 131 2250 3001 2521 3249 118 160 2447 3118 0 0 1375 1887 449 146 82 92 78 88 5251 5565 .75 1.334 1.274 1.383 1.294 1.741 80 365 1.277 .89 100 3930 8110 35 45 238 248 0 3041 127 2914 1.295 3154 3027 .772 1.237 .373 .307
15 913 1691 71 129 842 1562 924 1646 92 180 853 1517 0 0 413 835 101 209 94 98 92 88 2404 2370 .539 1.855 1.778 1.89 1.746 1.584 52 303 1.916 .95 90 4090 8100 34 43 254 263 0 1642 125 1517 1.801 1598 1473 .555 1.727 .849 .788
16 1224 6846 73 136 1151 6710 1332 7150 91 224 1259 7014 0 0 668 3281 104 512 90 96 83 90 7861 8273 .172 5.83 5.571 6.434 5.641 1.723 80 451 5.739 .95 110 4240 8110 34 45 268 279 0 6647 132 6515 5.66 6942 6810 .177 5.409 2.501 2.435
17 1282 837 77 142 1205 695 1404 862 85 184 1327 720 0 0 589 320 72 356 96 81 92 51 1900 2047 1.734 .577 .543 .647 .589 1.744 80 367 .583 .93 100 4400 8120 36 46 285 295 0 813 138 675 .56 837 699 1.786 .527 -.837 -.925
18 877 1826 75 133 802 1693 982 1921 78 167 907 1788 0 0 405 795 26 269 95 95 95 91 2495 2695 .474 2.111 1.971 2.196 2.146 1.448 80 360 2.117 .96 100 4550 8130 37 47 300 310 0 1773 129 1644 2.049 1865 1736 .488 1.914 1.035 .937
19 192 196 73 143 119 53 108 156 77 169 35 13 0 0 213 136 25 258 60 8 42 2 172 48 2.245 .445 .371 .709 .752 3.957 80 393 5.736 .36 100 4710 8120 36 46 316 326 -50 190 139 51 .432 151 13 2.313 .361 -1.21 -1.471
20 851 739 75 136 776 603 792 775 76 147 717 639 0 0 501 343 17 52 92 94 92 92 1379 1356 1.287 .777 .891 .849 .804 1.599 52 313 .74 .94 90 4870 8120 36 45 332 341 0 717 132 585 .754 752 620 1.326 .865 -.407 -.209

Total number of rows: 37632

Table truncated, full table size 8337 Kbytes.




Supplementary data files not provided
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