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Sample GSM39973 Query DataSets for GSM39973
Status Public on Feb 21, 2005
Title Testes 0553
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Testes 0553
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://jdemeter-smd.stanford.edu:8000/MicroArray/gifs/2001-02/13729.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 GPL1825
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
1 768 680 278 161 490 519 764 724 280 162 486 563 0 0 182 225 56 47 98 95 98 91 1009 1049 .944 1.059 1.158 .983 1.082 1.68 80 339 1.109 .9 100 1170 8410 72 82 56 66 0 544 129 415 .847 579 450 1.18 .927 -.239 -.11 -.239
2 958 1109 274 156 684 953 685 882 278 161 411 726 0 0 645 860 63 49 90 92 82 82 1637 1137 .718 1.393 1.766 1.369 1.43 1.974 52 148 1.383 .95 80 1310 8420 74 82 71 79 -100 887 125 762 1.115 706 581 .897 1.413 .499 .157
3 6034 5578 287 163 5747 5415 6098 6024 292 170 5811 5861 0 0 1602 1346 67 61 100 100 100 100 11162 11672 1.061 .942 1.009 .947 .938 1.226 80 275 .911 .98 100 1440 8410 72 82 83 93 0 4462 130 4332 .754 4819 4689 1.327 .807 -.408 -.31 -.408
4 1436 2218 289 176 1147 2042 1545 2717 289 183 1256 2541 0 0 497 926 58 95 100 100 100 100 3189 3797 .562 1.78 2.023 1.752 1.699 1.227 12 77 2.21 .93 50 1580 8420 75 80 99 104 -100 1774 141 1634 1.424 2174 2033 .702 1.618 .695 .51
5 1861 4582 284 166 1577 4416 1745 4387 290 184 1461 4221 0 0 476 1195 59 115 100 100 100 100 5993 5682 .357 2.8 2.889 2.826 2.879 1.188 80 316 2.851 .96 100 1710 8410 72 82 110 120 -100 3666 133 3533 2.24 3510 3377 .446 2.311 1.209 1.164
6 1674 2573 299 171 1375 2402 1587 2432 306 176 1288 2261 0 0 324 761 51 52 100 100 100 100 3777 3549 .572 1.747 1.755 1.713 1.764 1.25 12 72 1.999 .93 50 1860 8420 75 80 127 132 -100 2058 137 1922 1.398 1946 1809 .716 1.404 .49 .483
7 1710 3003 307 173 1403 2830 1869 3242 345 253 1562 3069 0 0 564 1161 176 324 92 90 91 90 4233 4631 .496 2.017 1.965 1.99 2.037 1.65 80 289 2.047 .97 100 1980 8400 71 81 137 147 0 2402 138 2264 1.614 2594 2455 .62 1.572 .69 .652 .69
8 1676 2231 317 171 1359 2060 1707 2138 405 348 1390 1967 0 0 459 869 247 447 92 92 91 90 3419 3357 .66 1.516 1.415 1.439 1.498 1.357 80 234 1.605 .94 100 2120 8400 71 81 151 161 -100 1785 137 1648 1.213 1710 1574 .825 1.132 .179 .278
9 787 838 294 170 493 668 754 797 354 277 460 627 0 0 292 433 194 315 86 75 61 48 1161 1087 .738 1.355 1.363 1.32 1.374 1.674 52 237 1.538 .92 90 2250 8380 69 78 164 173 0 670 136 534 1.084 638 502 .923 1.09 .116 .125 .116
10 790 789 275 160 515 629 787 827 276 177 512 667 0 0 183 293 64 113 100 95 96 91 1144 1179 .819 1.221 1.303 1.13 1.103 1.544 80 239 1.332 .9 100 2400 8390 70 80 179 189 0 631 128 503 .977 662 534 1.023 1.042 -.033 .06 -.033
11 3287 1256 270 164 3017 1092 3448 1244 274 180 3178 1080 0 0 826 460 59 115 100 98 100 95 4109 4258 2.763 .362 .34 .332 .359 1.579 80 222 .372 .94 100 2530 8380 69 79 192 202 0 1005 131 874 .29 995 864 3.454 .272 -1.788 -1.879 -1.788
12 1270 1933 270 157 1000 1776 1246 2051 272 164 976 1894 0 0 364 658 52 48 100 100 100 100 2776 2870 .563 1.776 1.941 1.757 1.685 1.283 52 172 1.819 .96 80 2660 8380 70 78 206 214 0 1546 126 1421 1.421 1641 1515 .704 1.552 .507 .635 .507
13 907 1627 266 154 641 1473 888 1604 270 159 622 1450 0 0 245 545 51 44 100 100 96 100 2114 2072 .435 2.298 2.331 2.327 2.341 1.434 80 260 2.395 .94 100 2800 8380 69 79 219 229 0 1302 123 1178 1.838 1283 1160 .544 1.865 .878 .899 .878
14 1087 1298 269 158 818 1140 1085 1367 273 161 816 1209 0 0 307 490 54 44 100 100 98 100 1958 2025 .718 1.394 1.482 1.328 1.443 1.461 80 243 1.46 .95 100 2940 8380 69 79 233 243 0 1038 126 912 1.115 1094 967 .897 1.185 .157 .245 .157
15 1485 2453 268 154 1217 2299 1538 2632 272 159 1270 2478 0 0 416 917 53 47 100 100 100 100 3516 3748 .529 1.889 1.951 1.818 1.932 1.414 52 204 1.98 .96 90 3070 8370 68 77 246 255 0 1962 123 1839 1.511 2106 1982 .662 1.561 .596 .642 .596
16 2035 3528 278 153 1757 3375 2063 3588 280 157 1785 3435 0 0 400 689 53 45 100 100 100 100 5132 5220 .521 1.921 1.924 1.926 1.938 1.191 80 304 1.9 .97 110 3200 8380 68 79 258 269 0 2822 122 2700 1.537 2870 2748 .651 1.539 .62 .622 .62
17 1310 2460 275 155 1035 2305 1308 2481 284 166 1033 2326 0 0 266 570 66 68 100 100 100 100 3340 3359 .449 2.227 2.252 2.232 2.262 1.265 52 242 2.247 .95 90 3330 8370 68 77 272 281 0 1968 124 1844 1.782 1985 1861 .561 1.801 .833 .849 .833
18 757 442 265 152 492 290 769 430 273 163 504 278 0 0 125 128 68 64 100 93 100 90 782 782 1.697 .589 .552 .534 .567 1.673 80 316 .616 .85 110 3470 8380 68 79 285 296 0 354 122 232 .472 344 222 2.121 .441 -1.085 -1.18 -1.085
19 773 3252 253 148 520 3104 761 3249 258 154 508 3101 0 0 166 531 53 46 100 100 100 100 3624 3609 .168 5.969 6.104 6.158 6.072 1.304 80 280 6 .92 110 3600 8380 68 79 298 309 0 2602 118 2483 4.775 2599 2481 .209 4.883 2.256 2.288 2.256
20 1807 3203 252 151 1555 3052 1826 3243 260 155 1574 3092 0 0 434 786 55 45 100 100 100 100 4607 4666 .51 1.963 1.964 1.98 1.996 1.246 80 248 1.984 .97 100 3730 8380 69 79 312 322 0 2562 121 2442 1.57 2594 2474 .637 1.572 .651 .652 .651

Total number of rows: 44160

Table truncated, full table size 10014 Kbytes.




Supplementary data files not provided
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