NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM84889 Query DataSets for GSM84889
Status Public on Nov 23, 2005
Title s3664, p320, 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 s3664, p320, Pax whole blood
Organism Homo sapiens
Characteristics s3664, p320, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23055.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
1 956 1554 167 157 789 1397 1008 1689 169 164 841 1532 0 0 378 680 38 62 98 100 96 100 2186 2373 .565 1.771 1.822 1.847 1.781 1.493 80 512 1.826 .95 110 2210 8430 30 41 48 59 0 1388 140 1247 1.581 1508 1368 .633 1.626 .661 .702
2 1356 2241 170 161 1186 2080 1350 2292 175 171 1180 2131 0 0 460 680 45 68 98 100 98 100 3266 3311 .57 1.754 1.806 1.789 1.792 1.306 80 421 1.679 .96 100 2370 8430 31 41 65 75 0 2001 144 1857 1.566 2046 1903 .639 1.612 .647 .689
3 968 1697 173 160 795 1537 1061 1853 180 167 888 1693 0 0 381 699 59 61 98 100 95 100 2332 2581 .517 1.933 1.907 2.06 1.979 1.661 80 392 1.918 .95 100 2540 8430 31 41 82 92 0 1515 143 1372 1.726 1654 1512 .579 1.702 .788 .767
4 1104 1894 172 159 932 1735 1172 2005 178 170 1000 1846 0 0 554 1001 66 76 90 98 87 97 2667 2846 .537 1.862 1.846 1.911 1.895 1.575 80 412 1.878 .94 110 2680 8430 30 41 95 106 0 1691 142 1549 1.662 1790 1648 .602 1.648 .733 .721
5 771 1231 179 180 592 1051 812 1304 192 211 633 1124 0 0 325 600 83 148 96 94 86 84 1643 1757 .563 1.775 1.776 1.773 1.843 1.849 52 313 1.84 .92 90 2830 8410 29 38 111 120 0 1099 161 938 1.585 1164 1004 .631 1.585 .665 .665
6 1294 3226 177 186 1117 3040 1276 3404 190 221 1099 3218 0 0 449 974 71 124 100 100 97 100 4157 4317 .367 2.722 2.928 2.892 2.759 1.418 80 449 2.679 .95 110 2990 8420 29 40 126 137 0 2880 166 2714 2.43 3039 2873 .412 2.614 1.281 1.386
7 1811 3050 173 183 1638 2867 1868 3148 179 204 1695 2965 0 0 705 1128 43 97 100 100 100 100 4505 4660 .571 1.75 1.749 1.795 1.813 1.315 80 433 1.741 .96 110 3150 8410 28 39 142 153 0 2723 163 2560 1.563 2811 2647 .64 1.562 .644 .643
8 1279 2332 172 156 1107 2176 1281 2537 179 167 1109 2381 0 0 515 970 47 65 100 100 100 100 3283 3490 .509 1.966 2.147 1.972 2.018 1.427 80 364 1.958 .94 100 3310 8410 29 39 159 169 0 2082 139 1943 1.755 2265 2126 .57 1.917 .812 .939
9 1884 2382 170 162 1714 2220 1890 2329 176 173 1720 2167 0 0 772 1026 48 66 100 100 100 100 3934 3887 .772 1.295 1.26 1.318 1.281 1.364 80 435 1.315 .95 110 3460 8410 28 39 173 184 0 2127 145 1982 1.156 2079 1935 .865 1.125 .21 .17
10 1975 3387 165 176 1810 3211 2013 3689 172 184 1848 3513 0 0 718 1233 38 65 100 100 100 100 5021 5361 .564 1.774 1.901 1.775 1.789 1.267 52 324 1.791 .96 90 3620 8420 30 39 190 199 0 3024 157 2867 1.584 3294 3137 .631 1.697 .664 .763
11 1707 2685 169 195 1538 2490 1665 2586 174 210 1496 2391 0 0 586 921 37 79 100 100 100 100 4028 3887 .618 1.619 1.598 1.655 1.61 1.382 80 460 1.624 .96 110 3780 8410 28 39 205 216 0 2397 174 2223 1.446 2309 2135 .692 1.427 .532 .513
12 1597 3119 168 196 1429 2923 1574 2427 173 211 1406 2231 0 0 967 2069 38 79 97 100 93 100 4352 3637 .489 2.045 1.587 2.203 2.064 1.787 80 345 2.121 .97 100 3940 8420 30 40 222 232 0 2785 175 2610 1.826 2167 1992 .548 1.417 .869 .503
13 1373 2183 168 198 1205 1985 1420 2118 174 209 1252 1920 0 0 595 1003 36 79 98 100 98 100 3190 3172 .607 1.647 1.534 1.678 1.61 1.456 80 338 1.671 .94 100 4080 8420 30 40 236 246 0 1949 177 1772 1.471 1891 1714 .68 1.369 .557 .453
14 3560 4229 165 196 3395 4033 3783 4144 174 211 3618 3948 0 0 1727 2283 55 90 100 100 100 100 7428 7566 .842 1.188 1.091 1.197 1.129 1.504 80 422 1.201 .95 110 4240 8400 27 38 251 262 0 3776 175 3601 1.061 3700 3525 .943 .974 .085 -.038
15 1655 2663 160 186 1495 2477 1709 2743 172 206 1549 2557 0 0 709 1089 60 91 100 100 98 100 3972 4106 .604 1.657 1.651 1.743 1.654 1.427 80 338 1.639 .97 100 4390 8420 30 40 267 277 0 2378 166 2212 1.479 2449 2283 .676 1.474 .565 .56
16 1727 5657 167 190 1560 5467 1826 5817 173 205 1659 5627 0 0 751 2227 49 90 99 100 97 100 7027 7286 .285 3.504 3.392 3.842 3.498 1.542 120 473 3.443 .98 120 4550 8410 28 40 282 294 0 5051 170 4881 3.129 5194 5024 .32 3.028 1.646 1.599
17 1880 1599 163 184 1717 1415 1776 1258 167 194 1613 1074 0 0 800 933 38 72 100 100 100 98 3132 2687 1.213 .824 .666 .733 .794 1.506 80 406 .899 .94 110 4710 8410 28 39 298 309 0 1428 164 1263 .736 1123 959 1.359 .595 -.443 -.75
18 1694 2554 162 184 1532 2370 1711 2631 165 197 1549 2447 0 0 656 904 35 75 100 100 100 100 3902 3996 .646 1.547 1.58 1.619 1.545 1.414 80 364 1.539 .95 100 4860 8410 29 39 314 324 0 2280 164 2116 1.381 2349 2185 .724 1.41 .466 .496
19 403 494 160 191 243 303 210 226 168 203 50 35 0 0 459 601 59 78 41 38 27 32 546 85 .802 1.247 .7 1.746 1.79 4.002 80 390 1.369 .88 100 5020 8410 29 39 330 340 -50 441 171 271 1.113 202 31 .898 .625 .155 -.678
20 1377 1720 163 188 1214 1532 1311 1623 171 203 1148 1435 0 0 753 1133 61 77 94 96 94 92 2746 2583 .792 1.262 1.25 1.108 1.15 1.98 52 315 1.375 .94 90 5190 8410 29 38 347 356 0 1536 168 1368 1.127 1449 1281 .888 1.116 .172 .158

Total number of rows: 37632

Table truncated, full table size 8574 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap