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Sample GSM84873 Query DataSets for GSM84873
Status Public on Nov 23, 2005
Title s4544, p800, CPT
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 s4544, p800, CPT
Organism Homo sapiens
Characteristics s4544, p800, CPT
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/25800.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 Oct 16, 2012
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 GPL3122
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 2366 4845 271 111 2095 4734 2426 5071 274 120 2155 4960 0 0 352 928 54 68 100 100 100 100 6829 7115 .443 2.26 2.302 2.243 2.27 1.127 80 535 2.327 .98 110 2240 8360 28 39 39 50 0 3670 84 3586 1.712 3842 3758 .584 1.744 .776 .802
2 2548 4290 269 107 2279 4183 2543 4321 271 123 2274 4214 0 0 244 559 57 92 100 100 100 100 6462 6488 .545 1.835 1.853 1.829 1.847 1.115 80 432 1.847 .99 110 2410 8370 29 40 56 67 0 3250 81 3169 1.39 3273 3192 .719 1.404 .476 .489
3 1653 2853 269 111 1384 2742 1802 2986 276 125 1533 2875 0 0 478 816 79 78 99 100 99 100 4126 4408 .505 1.981 1.875 2.057 1.996 1.257 120 460 1.958 .98 120 2570 8380 30 42 72 84 0 2161 84 2077 1.501 2262 2178 .666 1.421 .586 .507
4 3193 5288 269 117 2924 5171 3293 5653 285 132 3024 5536 0 0 466 1074 95 76 100 100 100 100 8095 8560 .565 1.768 1.831 1.745 1.756 1.154 80 427 1.805 .99 110 2720 8370 29 40 87 98 0 4006 89 3917 1.34 4283 4194 .746 1.387 .422 .472
5 1124 880 265 115 859 765 1109 875 270 127 844 760 0 0 163 143 60 70 100 100 100 100 1624 1604 1.123 .891 .9 .892 .888 1.218 80 409 .883 .96 110 2880 8360 28 39 103 114 0 667 87 580 .675 663 576 1.482 .682 -.568 -.552
6 1932 4405 267 115 1665 4290 2212 5136 269 123 1945 5021 0 0 696 1659 55 47 100 100 96 100 5955 6966 .388 2.577 2.581 2.728 2.557 1.378 120 404 2.551 .98 120 3040 8380 30 42 119 131 0 3337 87 3250 1.952 3891 3804 .512 1.956 .965 .968
7 3231 5870 271 130 2960 5740 3350 6201 273 147 3079 6071 0 0 563 1262 64 138 100 100 100 100 8700 9150 .516 1.939 1.972 1.918 1.928 1.127 80 374 1.963 .98 110 3180 8370 29 40 133 144 0 4447 98 4348 1.469 4698 4599 .681 1.494 .555 .579
8 1494 1778 274 133 1220 1645 1512 1747 280 156 1238 1614 0 0 162 236 64 145 100 100 100 100 2865 2852 .742 1.348 1.304 1.346 1.363 1.163 80 414 1.358 .97 110 3350 8370 29 40 150 161 0 1347 101 1246 1.021 1323 1223 .979 .988 .031 -.018
9 1447 2019 278 129 1169 1890 1424 1990 289 160 1146 1861 0 0 202 323 77 137 100 100 100 100 3059 3007 .619 1.617 1.624 1.613 1.635 1.208 80 409 1.651 .96 110 3490 8350 27 38 164 175 0 1530 98 1432 1.225 1508 1410 .816 1.23 .293 .299
10 4299 4437 286 139 4013 4298 4612 4746 295 166 4326 4607 0 0 1230 1156 81 138 100 100 100 100 8311 8933 .934 1.071 1.065 1.084 1.079 1.13 80 413 1.064 .99 110 3650 8360 28 39 180 191 0 3361 105 3256 .811 3595 3490 1.232 .807 -.302 -.31
11 2334 2865 270 123 2064 2742 2554 3131 274 132 2284 3008 0 0 717 926 60 75 100 100 100 100 4806 5292 .753 1.328 1.317 1.345 1.328 1.223 120 460 1.326 .98 120 3820 8360 28 40 197 209 0 2170 93 2077 1.006 2372 2279 .994 .998 .009 -.003
12 2910 3164 269 122 2641 3042 2989 3350 268 125 2720 3228 0 0 565 676 47 36 100 100 100 100 5683 5948 .868 1.152 1.187 1.147 1.14 1.127 80 356 1.151 .98 110 3970 8370 29 40 212 223 0 2397 92 2305 .873 2538 2445 1.146 .899 -.197 -.154
13 2116 2709 281 129 1835 2580 2134 2793 282 145 1853 2664 0 0 294 497 58 90 100 100 100 100 4415 4517 .711 1.406 1.438 1.391 1.406 1.168 80 410 1.382 .97 110 4120 8360 28 39 227 238 0 2052 98 1955 1.065 2116 2018 .939 1.089 .091 .123
14 8378 9668 282 137 8096 9531 8633 10195 290 185 8351 10058 0 0 1801 2297 85 272 100 100 100 100 17627 18409 .849 1.177 1.204 1.17 1.193 1.129 80 416 1.203 .99 110 4290 8360 28 39 244 255 0 7324 104 7220 .892 7723 7620 1.121 .912 -.165 -.132
15 3757 4166 283 138 3474 4028 3885 4333 290 195 3602 4195 0 0 778 793 92 312 100 100 100 100 7502 7797 .862 1.159 1.165 1.168 1.154 1.14 80 408 1.144 .98 110 4440 8360 28 39 259 270 0 3156 105 3052 .878 3283 3178 1.138 .882 -.187 -.181
16 3318 9582 286 144 3032 9438 3513 10069 299 228 3227 9925 0 0 542 2064 119 453 100 100 100 100 12470 13152 .321 3.113 3.076 3.07 3.124 1.138 80 462 3.186 .99 110 4600 8350 27 38 275 286 0 7259 109 7150 2.358 7628 7519 .424 2.33 1.238 1.22
17 4793 4370 280 127 4513 4243 4974 4604 289 169 4694 4477 0 0 865 850 87 333 100 100 100 100 8756 9171 1.064 .94 .954 .938 .94 1.104 80 441 .933 .98 110 4760 8360 28 39 291 302 0 3311 96 3214 .712 3488 3392 1.404 .723 -.49 -.469
18 2919 2237 280 115 2639 2122 2937 2235 291 130 2657 2120 0 0 286 326 80 84 100 100 100 100 4761 4777 1.244 .804 .798 .799 .787 1.165 80 399 .801 .98 110 4920 8360 28 39 307 318 0 1695 87 1608 .609 1693 1606 1.642 .604 -.715 -.726
19 480 256 277 121 203 135 282 131 302 135 5 10 0 0 494 331 185 79 20 21 17 17 338 15 1.504 .665 2 .701 .692 2.342 80 372 .478 .79 100 5050 8360 29 39 321 331 -50 194 92 102 .504 99 8 1.985 1.515 -.989 .599
20 3253 3558 270 118 2983 3440 3343 3583 286 125 3073 3465 0 0 816 920 165 38 100 100 100 100 6423 6538 .867 1.153 1.128 1.154 1.153 1.168 80 404 1.134 .98 110 5240 8370 29 40 339 350 0 2695 89 2606 .874 2714 2625 1.145 .854 -.195 -.227

Total number of rows: 37632

Table truncated, full table size 8743 Kbytes.




Supplementary data files not provided
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