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Sample GSM84927 Query DataSets for GSM84927
Status Public on Nov 23, 2005
Title s49C, 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 s49C, pNepal, Pax whole blood
Organism Homo sapiens
Characteristics s49C, pNepal, Pax whole blood
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2001-12/23083.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
1 827 1696 110 186 717 1510 814 1384 112 192 704 1198 0 0 282 857 19 59 100 100 100 100 2227 1902 .475 2.106 1.702 2.016 2.036 1.344 80 393 2.373 .95 100 2120 8550 31 41 36 46 0 1295 142 1153 1.608 1056 915 .622 1.299 .685 .377
2 1160 2305 112 177 1048 2128 1218 2372 111 185 1106 2195 0 0 341 741 19 53 100 100 100 100 3176 3301 .492 2.031 1.985 2.02 2.018 1.24 80 380 2.059 .98 100 2280 8560 32 42 52 62 0 1760 135 1624 1.55 1811 1676 .645 1.515 .632 .599
3 1018 3524 110 185 908 3339 986 3302 110 190 876 3117 0 0 373 1547 17 58 100 100 100 100 4247 3993 .272 3.677 3.558 3.641 3.7 1.206 80 396 3.854 .98 100 2430 8560 32 42 67 77 0 2690 141 2549 2.807 2521 2379 .356 2.716 1.489 1.442
4 966 1780 110 188 856 1592 1048 1750 110 194 938 1562 0 0 343 681 18 59 98 100 97 100 2448 2500 .538 1.86 1.665 1.897 1.844 1.432 80 403 1.918 .97 100 2600 8550 31 41 84 94 0 1359 144 1215 1.42 1336 1192 .704 1.271 .506 .346
5 464 836 109 191 355 645 472 776 111 197 363 585 0 0 247 411 19 57 91 95 88 93 1000 948 .55 1.817 1.612 1.895 1.794 1.505 80 358 1.859 .94 100 2760 8560 32 42 100 110 0 638 146 492 1.387 592 447 .721 1.23 .472 .299
6 854 2755 110 197 744 2558 891 2848 112 204 781 2651 0 0 230 589 19 59 100 100 100 100 3302 3432 .291 3.438 3.394 3.622 3.386 1.406 80 423 3.445 .97 110 2910 8550 30 41 114 125 0 2103 150 1953 2.625 2174 2024 .381 2.591 1.392 1.374
7 1340 2083 109 208 1231 1875 1418 2132 110 212 1309 1924 0 0 489 624 19 62 98 100 98 100 3106 3233 .657 1.523 1.47 1.596 1.46 1.436 80 373 1.506 .97 100 3080 8550 31 41 132 142 0 1590 159 1431 1.163 1627 1469 .86 1.122 .217 .166
8 862 1450 108 201 754 1249 878 1455 109 201 770 1254 0 0 169 390 19 56 100 100 100 100 2003 2024 .604 1.656 1.629 1.622 1.639 1.291 80 401 1.744 .96 110 3230 8550 30 41 146 157 0 1107 153 953 1.265 1111 957 .791 1.243 .339 .314
9 1320 1179 105 206 1215 973 1548 1266 112 210 1443 1060 0 0 655 525 51 71 93 93 92 90 2188 2503 1.249 .801 .735 .836 .788 1.628 80 419 .79 .94 110 3380 8540 29 40 161 172 0 900 157 743 .611 966 809 1.636 .561 -.71 -.835
10 1275 1454 105 207 1170 1247 1221 1466 113 219 1116 1259 0 0 326 357 53 79 100 100 100 100 2417 2375 .938 1.066 1.128 1.064 1.063 1.259 52 304 1.097 .95 90 3530 8540 30 39 177 186 0 1110 158 952 .814 1119 961 1.229 .861 -.298 -.216
11 1033 1345 105 219 928 1126 1123 1350 108 227 1018 1131 0 0 349 425 23 68 97 97 97 97 2054 2149 .824 1.213 1.111 1.237 1.156 1.35 80 458 1.211 .96 110 3690 8540 29 40 192 203 0 1027 167 860 .926 1031 863 1.08 .848 -.111 -.238
12 851 1337 105 225 746 1112 814 1412 106 229 709 1187 0 0 395 498 20 63 95 96 95 93 1858 1896 .671 1.491 1.674 1.524 1.424 1.517 80 363 1.471 .95 100 3860 8540 30 40 210 220 0 1021 172 849 1.138 1078 906 .879 1.278 .186 .354
13 963 1426 106 220 857 1206 1009 1428 108 225 903 1208 0 0 235 398 20 66 100 100 100 100 2063 2111 .711 1.407 1.338 1.389 1.386 1.294 80 384 1.499 .95 110 4000 8550 30 41 223 234 0 1089 168 921 1.074 1090 922 .931 1.021 .103 .03
14 2686 2047 107 215 2579 1832 2827 2075 109 220 2720 1860 0 0 725 517 21 64 100 100 100 100 4411 4580 1.408 .71 .684 .712 .706 1.226 80 428 .704 .98 110 4160 8540 29 40 239 250 0 1563 164 1398 .542 1584 1420 1.844 .522 -.883 -.938
15 1004 1323 107 223 897 1100 1092 1288 108 226 985 1065 0 0 326 411 20 63 100 100 100 100 1997 2050 .815 1.226 1.081 1.239 1.154 1.43 80 350 1.261 .94 100 4320 8540 30 40 256 266 0 1010 170 840 .936 983 813 1.068 .825 -.095 -.277
16 1777 6910 105 224 1672 6686 1803 6806 106 233 1698 6582 0 0 436 1569 18 72 100 100 100 100 8358 8280 .25 3.999 3.876 4.081 3.934 1.218 80 407 4.025 .98 110 4470 8540 29 40 270 281 0 5275 171 5104 3.053 5195 5024 .328 2.959 1.61 1.565
17 1762 1548 104 232 1658 1316 1811 1469 106 236 1707 1237 0 0 742 798 17 73 100 98 98 97 2974 2944 1.26 .794 .725 .781 .657 1.834 80 364 .93 .85 100 4630 8540 30 40 287 297 0 1182 177 1005 .606 1121 944 1.65 .553 -.723 -.854
18 1313 3127 104 239 1209 2888 1324 3033 111 251 1220 2794 0 0 430 1296 52 87 100 100 100 100 4097 4014 .419 2.389 2.29 2.333 2.332 1.303 80 390 2.568 .95 100 4780 8540 30 40 302 312 0 2387 182 2205 1.823 2315 2133 .548 1.748 .867 .806
19 1652 5246 108 251 1544 4995 1364 4609 145 284 1256 4358 0 0 1019 2822 120 126 100 100 100 100 6539 5614 .309 3.235 3.47 3.5 3.291 1.333 12 80 3.095 .96 50 4920 8520 30 35 318 323 -100 4005 192 3813 2.47 3518 3327 .405 2.649 1.304 1.405
20 2141 6969 105 254 2036 6715 2125 5994 108 259 2020 5740 0 0 960 4338 20 76 100 100 100 100 8751 7760 .303 3.298 2.842 2.937 3.305 1.418 52 336 3.731 .96 90 5090 8540 30 39 333 342 0 5320 194 5126 2.518 4576 4382 .397 2.169 1.332 1.117

Total number of rows: 37632

Table truncated, full table size 8486 Kbytes.




Supplementary data files not provided
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