NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM84904 Query DataSets for GSM84904
Status Public on Nov 23, 2005
Title s47C, pNepal, 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 s47C, pNepal, Pax whole blood
Organism Homo sapiens
Characteristics s47C, pNepal, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23131.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
1 574 1450 82 137 492 1313 593 1430 83 145 511 1293 0 0 175 429 17 62 100 100 100 100 1805 1804 .375 2.669 2.53 2.715 2.599 1.474 80 417 3.715 .83 100 1930 8120 33 43 42 52 0 1198 113 1085 2.206 1182 1069 .453 2.091 1.141 1.064
2 755 2034 81 139 674 1895 771 2114 83 143 690 1975 0 0 249 509 17 58 100 100 100 100 2569 2665 .356 2.812 2.862 2.959 2.815 1.379 80 397 2.822 .95 100 2090 8130 34 44 58 68 0 1681 115 1566 2.324 1747 1632 .43 2.366 1.216 1.242
3 655 3047 80 139 575 2908 671 3059 81 146 591 2920 0 0 260 945 16 61 100 100 98 100 3483 3511 .198 5.057 4.941 5.57 5.245 1.492 80 366 4.907 .95 100 2250 8120 33 43 74 84 0 2518 115 2403 4.18 2528 2413 .239 4.083 2.063 2.03
4 622 1600 81 142 541 1458 548 1574 82 145 467 1432 0 0 425 910 16 46 91 98 90 95 1999 1899 .371 2.695 3.066 3.233 2.773 2.097 80 350 2.583 .92 100 2410 8120 33 43 90 100 0 1322 117 1205 2.227 1301 1183 .449 2.534 1.155 1.342
5 384 952 83 142 301 810 368 840 84 147 285 698 0 0 231 697 18 47 95 96 91 95 1111 983 .372 2.691 2.449 2.701 2.891 2.118 80 350 3.149 .88 100 2560 8120 33 43 105 115 0 787 117 669 2.224 694 577 .45 2.024 1.153 1.017
6 586 2284 82 147 504 2137 609 2185 84 151 527 2038 0 0 263 970 18 46 93 97 93 97 2641 2565 .236 4.24 3.867 4.24 4.199 1.575 80 351 4.171 .96 100 2720 8120 33 43 121 131 0 1888 121 1766 3.504 1806 1684 .285 3.196 1.809 1.676
7 1061 2396 81 145 980 2251 1045 2474 82 148 964 2329 0 0 540 1015 17 47 100 100 96 100 3231 3293 .435 2.297 2.416 2.624 2.288 1.619 80 418 2.279 .95 110 2870 8120 32 43 135 146 0 1980 120 1860 1.898 2045 1925 .527 1.997 .925 .998
8 606 1429 83 137 523 1292 634 1453 89 140 551 1316 0 0 187 383 66 51 98 100 95 100 1815 1867 .405 2.47 2.388 2.527 2.378 1.422 80 367 2.463 .9 100 3030 8120 33 43 152 162 0 1181 113 1068 2.042 1201 1088 .49 1.974 1.03 .981
9 1267 1926 84 137 1183 1789 1368 2060 98 153 1284 1923 0 0 754 897 81 87 92 96 91 93 2972 3207 .661 1.512 1.498 1.757 1.538 2.025 80 445 1.423 .93 110 3190 8110 31 42 167 178 0 1592 113 1479 1.25 1702 1589 .8 1.238 .322 .308
10 917 1544 84 134 833 1410 747 1316 108 173 663 1182 0 0 695 819 99 149 90 98 82 96 2243 1845 .591 1.693 1.783 2.216 1.823 2.243 52 287 1.537 .91 90 3350 8100 31 40 184 193 0 1276 111 1165 1.399 1088 977 .715 1.473 .484 .559
11 601 1599 77 130 524 1469 568 1620 86 146 491 1490 0 0 390 895 50 91 83 91 78 87 1993 1981 .357 2.803 3.035 2.851 2.64 1.583 80 366 2.676 .93 100 3500 8110 32 42 199 209 0 1321 107 1214 2.317 1339 1231 .432 2.508 1.212 1.327
12 691 1557 80 136 611 1421 723 1503 87 150 643 1367 0 0 254 657 42 88 98 98 96 98 2032 2010 .43 2.326 2.126 2.348 2.396 1.436 52 302 2.412 .94 90 3650 8110 32 41 214 223 0 1287 112 1174 1.922 1242 1130 .52 1.757 .943 .813
13 770 1717 77 137 693 1580 706 1507 81 145 629 1370 0 0 515 992 33 67 90 96 88 93 2273 1999 .439 2.28 2.178 2.423 2.429 1.641 80 422 2.225 .95 110 3810 8110 31 42 229 240 0 1419 113 1306 1.884 1245 1132 .531 1.8 .914 .848
14 1851 1817 77 132 1774 1685 1726 1710 79 134 1649 1578 0 0 1248 1106 17 45 95 96 93 92 3459 3227 1.053 .95 .957 1.087 .971 2.559 80 410 .923 .94 110 3960 8120 32 43 244 255 0 1502 109 1393 .785 1413 1304 1.274 .791 -.349 -.339
15 633 1171 79 129 554 1042 659 1216 81 133 580 1087 0 0 386 589 20 49 91 98 90 96 1596 1667 .532 1.881 1.874 2.025 1.864 1.57 80 349 1.832 .94 100 4120 8110 32 42 261 271 0 968 107 861 1.554 1005 898 .643 1.549 .636 .631
16 1180 4243 79 131 1101 4112 1268 4331 93 162 1189 4200 0 0 574 2035 101 233 90 96 87 92 5213 5389 .268 3.735 3.532 3.78 3.658 1.438 80 405 3.667 .95 110 4270 8110 31 42 275 286 0 3507 108 3398 3.087 3579 3471 .324 2.919 1.626 1.546
17 1411 1337 77 130 1334 1207 1386 1279 84 144 1309 1149 0 0 835 682 52 103 92 96 91 92 2541 2458 1.105 .905 .878 .987 .851 1.696 80 351 .871 .93 100 4420 8120 33 43 291 301 0 1105 107 998 .748 1057 950 1.337 .725 -.419 -.463
18 1254 3327 78 132 1176 3195 1267 3510 80 135 1189 3378 0 0 574 1291 16 42 100 100 100 100 4371 4567 .368 2.717 2.841 2.928 2.784 1.444 80 374 2.654 .97 100 4580 8120 33 43 307 317 0 2750 109 2640 2.245 2901 2792 .445 2.348 1.167 1.231
19 325 489 82 130 243 359 200 263 84 131 118 133 0 0 326 446 18 41 84 75 75 65 602 251 .677 1.477 1.127 1.433 1.211 2.843 32 148 .08 .16 60 4720 8120 35 41 323 329 0 404 107 297 1.221 217 110 .819 .932 .288 -.102
20 984 1648 81 131 903 1517 896 1455 83 131 815 1324 0 0 625 1041 24 41 100 98 98 98 2420 2139 .595 1.68 1.625 1.672 1.702 1.547 52 266 1.728 .94 80 4890 8120 34 42 339 347 0 1362 108 1254 1.388 1202 1094 .72 1.343 .473 .425

Total number of rows: 37632

Table truncated, full table size 8330 Kbytes.




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