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Sample GSM39887 Query DataSets for GSM39887
Status Public on Feb 21, 2005
Title Brain, frontal cortex 2271
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Brain, frontal cortex 2271
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-01/24155.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) pollack1@stanford.edu
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL1823
Series (1)
GSE2193 Normal_human_tissues

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
VALUE same as UNF_VALUE but with flagged values removed
LOG_RAT2N_MEDIAN 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
UNF_VALUE 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

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 VALUE LOG_RAT2N_MEDIAN UNF_VALUE
1 576 275 246 96 330 179 596 280 249 97 350 184 0 0 137 69 54 21 96 100 92 94 509 534 1.844 .542 .526 .5 .508 1.854 52 280 .436 .74 80 1340 7530 61 69 46 54 0 169 59 110 .333 172 113 3.005 .323 -1.587 -1.633 -1.587
2 486 329 242 96 244 233 493 324 249 98 251 228 0 0 107 50 54 22 92 100 90 100 477 479 1.047 .955 .908 .887 .853 1.51 52 300 .792 .71 90 1490 7530 60 69 60 69 0 202 59 143 .586 199 140 1.707 .557 -.771 -.844 -.771
3 1849 876 246 101 1603 775 2018 902 254 104 1772 801 0 0 541 298 62 29 100 100 98 100 2378 2573 2.068 .483 .452 .505 .488 1.884 52 324 .468 .9 90 1620 7530 60 69 73 82 0 537 62 475 .297 553 491 3.371 .277 -1.753 -1.85 -1.753
4 3676 8347 252 102 3424 8245 3649 8311 256 107 3397 8209 0 0 1405 3753 59 33 100 100 100 100 11669 11606 .415 2.408 2.417 2.332 2.732 1.618 52 367 2.641 .91 90 1780 7530 60 69 89 98 0 5121 63 5058 1.477 5099 5036 .677 1.483 .563 .568 .563
5 600 1485 255 108 345 1377 634 1398 256 111 379 1290 0 0 217 504 53 33 87 100 84 100 1722 1669 .251 3.991 3.404 4.082 3.916 1.593 32 230 4.172 .84 70 1930 7530 61 68 105 112 0 911 66 845 2.449 858 791 .408 2.088 1.292 1.062 1.292
6 512 311 266 111 246 200 531 321 268 112 265 210 0 0 128 63 56 26 90 100 84 100 446 475 1.23 .813 .792 .777 .685 1.767 32 171 .6 .69 60 2080 7540 63 69 121 127 0 191 68 123 .499 197 129 2.005 .486 -1.004 -1.04 -1.004
7 764 2938 252 103 512 2835 782 3314 256 105 530 3211 0 0 225 1018 54 28 94 100 92 100 3347 3741 .181 5.537 6.058 5.666 5.426 1.658 52 270 6.324 .86 90 2220 7530 60 69 133 142 0 1802 63 1739 3.397 2033 1970 .294 3.717 1.764 1.894 1.764
8 3979 4487 252 104 3727 4383 4471 5021 256 105 4219 4917 0 0 2170 2426 52 29 100 100 100 97 8110 9136 .85 1.176 1.165 1.093 1.139 2.377 80 325 1.171 .9 100 2370 7530 60 70 148 158 0 2753 64 2689 .721 3080 3017 1.386 .715 -.471 -.484 -.471
9 1100 1230 248 105 852 1125 1179 1417 252 110 931 1312 0 0 374 454 53 38 98 100 98 100 1977 2243 .757 1.32 1.409 1.368 1.264 1.781 52 244 1.365 .88 80 2510 7530 61 69 163 171 0 755 64 690 .81 869 805 1.234 .865 -.304 -.21 -.304
10 465 723 238 109 227 614 453 670 247 109 215 561 0 0 151 300 55 22 88 100 80 100 841 776 .37 2.705 2.609 2.625 2.739 1.738 52 246 2.861 .79 80 2660 7530 61 69 178 186 0 444 67 377 1.659 411 344 .603 1.601 .731 .679 .731
11 1074 1074 243 110 831 964 1114 1108 252 111 871 998 0 0 451 385 57 25 98 100 94 100 1795 1869 .862 1.16 1.146 1.36 1.155 2.194 52 274 1.099 .88 90 2800 7540 61 70 191 200 0 659 67 591 .712 680 612 1.405 .703 -.491 -.509 -.491
12 992 1332 253 109 739 1223 1083 1374 258 110 830 1265 0 0 378 510 54 25 98 100 94 100 1962 2095 .604 1.655 1.524 1.759 1.669 1.591 52 323 1.656 .89 90 2940 7530 60 69 205 214 0 817 67 750 1.015 843 776 .985 .935 .022 -.097 .022
13 776 995 253 113 523 882 806 993 261 113 553 880 0 0 323 475 54 24 90 100 86 100 1405 1433 .593 1.686 1.591 1.785 1.568 2.091 52 284 1.72 .89 80 3100 7530 61 69 222 230 0 610 69 541 1.035 609 540 .967 .976 .049 -.035 .049
14 540 278 259 115 281 163 559 270 264 117 300 155 0 0 172 57 56 25 87 100 84 100 444 455 1.724 .58 .517 .552 .476 2.242 32 214 .36 .61 70 3250 7530 61 68 237 244 0 171 71 100 .356 166 95 2.81 .317 -1.491 -1.658 -1.491
15 3935 6824 264 118 3671 6706 4055 7356 267 125 3791 7238 0 0 1406 1949 51 42 100 100 100 100 10377 11029 .547 1.827 1.909 1.898 1.805 1.333 52 310 1.891 .93 90 3390 7530 60 69 250 259 0 4187 72 4114 1.121 4513 4440 .892 1.171 .164 .228 .164
16 1680 3615 267 118 1413 3497 1842 3789 266 120 1575 3671 0 0 514 1095 52 26 100 100 98 100 4910 5246 .404 2.475 2.331 2.615 2.527 1.487 52 289 2.518 .93 90 3530 7530 60 69 264 273 0 2218 72 2145 1.518 2325 2252 .659 1.43 .602 .516 .602
17 424 256 269 119 155 137 425 247 274 121 156 128 0 0 113 75 56 27 88 94 67 94 292 284 1.131 .884 .821 .661 .627 2.453 52 254 .525 .42 80 3680 7530 61 69 280 288 0 157 73 84 .542 152 79 1.844 .503 -.883 -.99 -.883
18 459 236 271 114 188 122 485 213 273 117 214 99 0 0 144 76 54 26 81 93 71 90 310 313 1.541 .649 .463 .585 .37 3.598 32 198 .214 .3 70 3820 7530 61 68 294 301 0 145 70 75 .398 131 61 2.512 .284 -1.329 -1.817 -1.329
19 748 1475 277 117 471 1358 747 1277 280 119 470 1160 0 0 246 721 57 26 96 100 88 100 1829 1630 .347 2.883 2.468 2.94 2.929 1.668 52 306 3.109 .9 80 3970 7530 61 69 309 317 0 905 72 833 1.769 783 712 .565 1.514 .823 .599 .823
20 448 249 291 116 157 133 447 226 293 118 156 110 0 0 131 84 56 27 78 93 65 81 290 266 1.18 .847 .705 .673 .636 3.191 32 147 .379 .33 60 4130 7520 61 67 326 332 0 153 71 82 .52 139 67 1.924 .433 -.944 -1.209 -.944

Total number of rows: 43008

Table truncated, full table size 9555 Kbytes.




Supplementary data files not provided
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