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Sample GSM84935 Query DataSets for GSM84935
Status Public on Nov 23, 2005
Title s9939, p992, 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 s9939, p992, Pax whole blood
Organism Homo sapiens
Characteristics s9939, p992, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/22935.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
1 426 1085 179 385 247 700 440 1053 181 407 261 668 0 0 126 300 37 197 96 96 92 80 947 929 .353 2.834 2.559 3.098 2.836 1.851 52 349 3.3 .81 90 2290 8030 41 50 67 76 0 828 294 534 2.163 804 510 .462 1.954 1.113 .966
2 514 1703 179 394 335 1309 531 1757 183 410 352 1363 0 0 138 473 41 137 100 100 97 100 1644 1715 .256 3.907 3.872 4.069 4.036 1.334 80 374 3.995 .94 100 2450 8050 43 53 83 93 0 1300 301 999 2.983 1341 1040 .335 2.956 1.577 1.564
3 544 2521 201 404 343 2117 439 2034 203 436 238 1630 0 0 291 1613 46 159 87 97 78 93 2460 1868 .162 6.172 6.849 6.721 6.18 1.953 80 354 5.979 .95 100 2600 8050 43 53 98 108 0 1924 308 1616 4.711 1553 1244 .212 5.228 2.236 2.386
4 407 984 213 398 194 586 381 949 218 425 168 551 0 0 138 364 42 151 88 90 71 75 780 719 .331 3.021 3.28 3.202 3.192 1.729 80 420 3.387 .84 100 2760 8060 44 54 114 124 0 751 304 447 2.306 724 421 .434 2.504 1.205 1.324
5 517 927 225 420 292 507 560 976 229 428 335 556 0 0 117 273 41 127 100 84 93 84 799 891 .576 1.736 1.66 1.665 1.552 1.547 32 170 2.251 .86 60 2920 8040 44 50 132 138 0 708 321 387 1.325 745 424 .754 1.267 .406 .341
6 395 1617 204 406 191 1211 406 1729 204 418 202 1323 0 0 101 456 41 123 90 100 83 100 1402 1525 .158 6.34 6.55 6.615 6.092 1.524 80 407 6.179 .88 100 3100 8060 44 54 148 158 0 1234 310 924 4.84 1320 1010 .207 5 2.275 2.322
7 774 2279 196 442 578 1837 791 2354 201 483 595 1912 0 0 222 619 57 219 98 98 98 97 2415 2507 .315 3.178 3.213 3.216 3.193 1.291 80 458 3.211 .95 110 3240 8040 41 52 161 172 0 1740 337 1402 2.426 1797 1460 .412 2.453 1.279 1.295
8 433 1079 204 481 229 598 429 1058 212 545 225 577 0 0 70 206 76 264 100 96 87 56 827 802 .383 2.611 2.564 2.592 2.483 1.507 32 196 2.803 .89 70 3410 8080 47 54 180 187 0 824 367 456 1.993 808 440 .502 1.958 .995 .969
9 614 1803 177 405 437 1398 598 1516 186 433 421 1111 0 0 174 896 59 170 100 100 100 98 1835 1532 .313 3.199 2.639 2.901 2.759 1.487 80 529 3.896 .93 110 3540 8040 41 52 191 202 0 1376 309 1067 2.442 1157 848 .409 2.014 1.288 1.01
10 642 1561 195 418 447 1143 606 1655 200 472 411 1237 0 0 246 572 71 227 90 90 87 90 1590 1648 .391 2.557 3.01 2.703 2.58 1.457 32 172 2.591 .92 60 3690 8060 46 52 209 215 0 1192 319 873 1.952 1263 944 .512 2.298 .965 1.2
11 656 1497 181 355 475 1142 659 1442 189 392 478 1087 0 0 123 389 50 176 100 100 100 100 1617 1565 .416 2.404 2.274 2.365 2.42 1.35 80 484 2.71 .91 110 3860 8030 40 51 223 234 0 1143 271 872 1.835 1101 830 .545 1.736 .876 .796
12 453 1102 182 376 271 726 504 1115 188 387 322 739 0 0 183 556 48 128 82 73 73 71 997 1061 .373 2.679 2.295 2.406 2.417 2.564 52 275 3.046 .89 80 4010 8030 42 50 240 248 0 841 287 554 2.045 851 564 .489 1.752 1.032 .809
13 583 1536 185 392 398 1144 603 1542 189 411 418 1150 0 0 143 369 49 134 100 100 98 100 1542 1568 .348 2.874 2.751 2.958 2.777 1.377 80 412 2.972 .93 100 4180 8040 42 52 256 266 0 1173 299 873 2.194 1177 878 .456 2.1 1.134 1.07
14 1960 1966 185 449 1775 1517 1887 1761 194 454 1702 1312 0 0 908 732 55 149 100 98 100 97 3292 3014 1.17 .855 .771 .866 .864 1.444 80 380 .841 .96 110 4340 8050 42 53 271 282 0 1501 343 1158 .652 1344 1002 1.533 .588 -.616 -.765
15 705 1985 184 491 521 1494 714 1932 200 541 530 1441 0 0 165 610 73 264 100 100 98 98 2015 1971 .349 2.868 2.719 2.782 2.872 1.32 52 253 3.32 .91 80 4480 8030 42 50 287 295 0 1515 375 1140 2.189 1475 1100 .457 2.075 1.13 1.053
16 1142 8810 184 590 958 8220 1145 9173 192 628 961 8583 0 0 259 1793 58 248 100 100 100 100 9178 9544 .117 8.58 8.931 8.729 8.749 1.174 80 453 8.454 .98 110 4650 8030 40 51 302 313 0 6725 450 6275 6.55 7002 6552 .153 6.818 2.711 2.769
17 1205 1472 191 591 1014 881 1178 1459 196 619 987 868 0 0 236 332 65 229 100 96 100 90 1895 1855 1.151 .869 .879 .798 .861 1.563 52 300 .963 .85 90 4790 8040 42 51 317 326 0 1124 451 673 .663 1114 663 1.508 .671 -.592 -.575
18 835 2715 166 425 669 2290 849 2598 176 455 683 2173 0 0 175 803 60 197 100 100 100 100 2959 2856 .292 3.423 3.182 3.34 3.362 1.25 80 424 3.621 .97 100 4960 8040 42 52 334 344 0 2073 324 1748 2.613 1983 1659 .383 2.429 1.386 1.28
19 253 469 168 375 85 94 189 407 175 390 21 32 0 0 182 274 51 153 33 23 22 12 179 53 .904 1.106 1.524 1.67 1.518 4.299 80 395 2.175 .7 100 5120 8030 41 51 350 360 -50 358 286 72 .844 311 24 1.185 1.163 -.244 .218
20 950 1264 183 363 767 901 978 1295 189 378 795 932 0 0 229 279 53 145 100 100 100 96 1668 1727 .851 1.175 1.172 1.164 1.157 1.447 32 212 1.263 .91 70 5280 8030 42 49 367 374 0 965 277 688 .897 989 711 1.115 .895 -.157 -.16

Total number of rows: 37632

Table truncated, full table size 8390 Kbytes.




Supplementary data files not provided
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