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Sample GSM84862 Query DataSets for GSM84862
Status Public on Nov 23, 2005
Title s3434, p814, 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 s3434, p814, Pax whole blood
Organism Homo sapiens
Characteristics s3434, p814, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23119.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
1 523 1278 94 148 429 1130 531 1291 95 158 437 1143 0 0 180 446 18 66 100 100 100 98 1559 1580 .38 2.634 2.616 2.679 2.618 1.321 80 417 2.72 .95 100 1730 8390 34 44 37 47 0 730 85 646 1.505 738 653 .664 1.495 .59 .58
2 586 2002 93 133 493 1869 597 2137 94 147 504 2004 0 0 169 661 20 65 100 100 100 100 2362 2508 .264 3.791 3.976 3.796 3.824 1.371 80 446 3.899 .95 110 1890 8400 34 45 52 63 0 1144 76 1068 2.166 1221 1145 .462 2.272 1.115 1.184
3 441 1496 93 131 348 1365 485 1572 96 143 392 1441 0 0 173 536 22 59 96 97 95 97 1713 1833 .255 3.922 3.676 4.285 3.972 1.619 80 465 3.85 .94 110 2050 8390 33 44 68 79 0 855 75 780 2.241 898 823 .446 2.101 1.164 1.071
4 586 1674 92 135 494 1539 622 1746 95 144 530 1611 0 0 269 700 21 62 97 100 95 100 2033 2141 .321 3.115 3.04 3.422 3.275 1.545 80 382 3.092 .95 100 2210 8390 34 44 85 95 0 957 77 879 1.78 998 921 .562 1.737 .832 .797
5 338 700 93 135 245 565 326 632 95 143 233 497 0 0 125 389 21 59 96 100 96 94 810 730 .434 2.306 2.133 2.245 2.43 2.139 52 320 2.816 .84 90 2350 8390 34 43 99 108 0 400 77 323 1.318 361 284 .759 1.219 .398 .286
6 577 2929 95 142 482 2787 575 3149 96 145 480 3007 0 0 237 1155 20 60 100 100 98 100 3269 3487 .173 5.782 6.265 6.024 6.012 1.431 80 390 5.772 .95 100 2520 8390 34 44 116 126 0 1674 81 1593 3.304 1799 1718 .303 3.58 1.724 1.84
7 1130 3087 97 140 1033 2947 1258 3186 98 145 1161 3046 0 0 514 1447 20 58 98 100 98 100 3980 4207 .351 2.853 2.624 2.91 2.885 1.327 80 408 2.871 .97 110 2680 8390 33 44 131 142 0 1764 80 1684 1.63 1821 1741 .613 1.499 .705 .584
8 705 1753 97 146 608 1607 727 1842 98 154 630 1696 0 0 209 577 23 62 100 100 100 100 2215 2326 .378 2.643 2.692 2.599 2.63 1.365 80 431 2.69 .95 110 2830 8380 32 43 146 157 0 1002 83 918 1.51 1053 969 .662 1.538 .595 .621
9 1522 3242 94 136 1428 3106 1731 3739 96 150 1637 3603 0 0 786 1655 24 70 95 97 93 95 4534 5240 .46 2.175 2.201 2.262 2.175 1.489 80 424 2.202 .96 110 2990 8380 32 43 162 173 0 1853 78 1775 1.243 2137 2059 .805 1.258 .314 .331
10 990 2682 92 131 898 2551 749 2113 93 147 657 1982 0 0 717 1779 20 69 92 100 92 98 3449 2639 .352 2.841 3.017 3.068 2.868 1.632 80 338 2.718 .96 100 3150 8390 34 44 179 189 0 1533 75 1458 1.623 1207 1133 .616 1.724 .699 .786
11 898 2568 89 129 809 2439 876 2694 91 144 787 2565 0 0 609 1552 19 67 90 100 87 98 3248 3352 .332 3.015 3.259 3.261 3.063 1.542 80 404 2.906 .96 110 3290 8390 33 44 192 203 0 1467 74 1394 1.723 1539 1466 .58 1.862 .785 .897
12 979 2691 90 127 889 2564 707 2229 94 143 617 2102 0 0 885 2107 23 76 88 98 83 96 3453 2719 .347 2.884 3.407 3.308 2.864 1.675 80 378 2.678 .96 100 3460 8380 33 43 210 220 0 1538 73 1465 1.648 1274 1201 .607 1.947 .721 .961
13 946 2545 93 130 853 2415 875 2541 96 145 782 2411 0 0 742 1809 26 76 83 92 82 92 3268 3193 .353 2.831 3.083 2.879 2.832 1.752 80 414 2.715 .96 110 3620 8380 32 43 225 236 0 1454 74 1380 1.618 1452 1378 .618 1.762 .694 .817
14 2152 5015 89 137 2063 4878 1376 3595 92 150 1287 3458 0 0 2102 4575 24 82 88 97 82 93 6941 4745 .423 2.365 2.687 3.175 2.443 2.669 80 420 2.317 .95 110 3770 8370 31 42 240 251 0 2866 78 2787 1.351 2054 1976 .74 1.535 .434 .619
15 1000 2913 90 142 910 2771 909 2316 92 154 819 2174 0 0 728 2232 20 71 87 100 83 95 3681 2993 .328 3.045 2.654 3.369 2.96 1.694 80 344 3.115 .96 100 3930 8380 33 43 257 267 0 1665 81 1583 1.74 1323 1242 .575 1.517 .799 .601
16 873 4945 89 146 784 4799 906 4923 91 159 817 4777 0 0 621 3350 21 66 89 100 82 98 5583 5594 .163 6.121 5.847 6.744 6.111 1.869 120 438 6.139 .94 120 4080 8380 32 44 271 283 0 2826 83 2742 3.498 2813 2730 .286 3.341 1.806 1.74
17 993 1077 89 142 904 935 1014 1081 91 156 925 939 0 0 652 581 20 67 92 96 90 91 1839 1864 .967 1.034 1.015 1.221 1.079 1.937 80 344 .959 .95 100 4230 8370 32 42 287 297 0 615 81 534 .591 618 537 1.692 .58 -.759 -.786
18 685 1936 87 144 598 1792 665 2092 90 155 578 1948 0 0 507 1258 20 68 81 92 78 91 2390 2526 .334 2.997 3.37 3.42 3.021 2.358 80 362 2.847 .95 100 4390 8380 33 43 303 313 0 1106 82 1024 1.712 1195 1113 .584 1.926 .776 .945
19 163 222 88 146 75 76 104 174 94 160 16 28 0 0 154 138 37 72 38 40 27 25 151 44 .987 1.013 1.75 2.081 1.631 3.569 80 395 1.175 .62 100 4550 8380 33 43 319 329 -50 127 83 43 .579 99 16 1.727 1 -.788 0
20 704 816 90 157 614 659 667 795 98 172 577 638 0 0 312 295 48 80 100 100 100 93 1273 1215 .932 1.073 1.106 1.093 1.073 1.287 32 195 1.307 .81 70 4710 8370 33 40 336 343 0 466 90 377 .613 454 365 1.631 .632 -.705 -.662

Total number of rows: 37632

Table truncated, full table size 8460 Kbytes.




Supplementary data files not provided
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