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Sample GSM39903 Query DataSets for GSM39903
Status Public on Feb 21, 2005
Title Testes 1068
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Testes 1068
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-01/24778.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
1 226 469 119 73 107 396 220 509 121 74 101 436 0 0 67 147 27 12 88 100 76 100 503 537 .27 3.701 4.317 4.146 3.724 2.199 52 356 4.125 .72 90 1560 8330 44 53 51 60 0 375 58 317 2.961 407 349 .338 3.453 1.566 1.788 1.566
2 201 108 121 77 80 31 200 106 125 79 79 29 0 0 42 21 27 15 92 76 73 48 111 108 2.581 .388 .367 .369 .357 2.205 52 300 .245 .45 90 1710 8330 44 53 66 75 0 86 62 25 .31 85 23 3.226 .294 -1.69 -1.768 -1.69
3 560 432 130 84 430 348 580 421 132 87 450 337 0 0 204 162 29 16 94 100 94 98 778 787 1.236 .809 .749 .874 .853 1.824 52 323 .829 .93 90 1840 8330 44 53 79 88 0 346 67 278 .647 337 270 1.545 .599 -.627 -.739 -.627
4 1980 3540 127 82 1853 3458 2194 3669 128 83 2067 3587 0 0 894 1318 28 15 100 100 100 100 5311 5654 .536 1.866 1.735 2.036 1.829 1.491 52 328 1.813 .95 90 1990 8340 45 54 94 103 0 2832 66 2766 1.493 2935 2870 .67 1.388 .578 .473 .578
5 275 203 125 79 150 124 281 208 128 79 156 129 0 0 96 62 26 14 88 94 82 92 274 285 1.21 .827 .827 .873 .812 1.782 52 272 .723 .86 80 2140 8330 45 53 110 118 0 162 63 99 .661 166 103 1.512 .662 -.597 -.596 -.597
6 202 110 131 84 71 26 200 109 136 84 69 25 0 0 56 20 47 16 65 73 34 38 97 94 2.731 .366 .362 .347 .312 2.838 52 340 .104 .3 90 2280 8330 44 53 123 132 0 88 67 21 .293 87 20 3.413 .29 -1.771 -1.787 -1.771
7 403 271 132 84 271 187 415 306 138 87 283 222 0 0 134 84 47 18 88 92 88 92 458 505 1.449 .69 .784 .676 .645 2.296 52 280 .648 .87 90 2430 8330 44 53 138 147 0 217 67 150 .552 245 178 1.811 .628 -.857 -.672 -.857
8 1573 2431 133 86 1440 2345 1612 2668 134 87 1479 2582 0 0 829 1399 27 19 98 98 97 98 3785 4061 .614 1.628 1.746 1.593 1.617 1.647 80 342 1.661 .97 100 2570 8330 44 54 152 162 0 1945 69 1876 1.303 2134 2066 .768 1.397 .382 .482 .382
9 490 374 132 90 358 284 521 389 131 90 389 299 0 0 172 120 28 20 98 100 94 94 642 688 1.261 .793 .769 .801 .758 1.814 52 254 .751 .93 80 2720 8340 46 54 168 176 0 299 72 227 .635 311 239 1.576 .615 -.656 -.702 -.656
10 221 112 134 91 87 21 218 112 134 92 84 21 0 0 99 28 30 16 71 57 61 28 108 105 4.143 .241 .25 .37 .325 3.314 52 254 .193 .54 80 2860 8330 45 53 182 190 0 90 73 17 .193 90 17 5.179 .2 -2.373 -2.322 -2.373
11 431 736 133 94 298 642 372 720 135 95 239 626 0 0 231 412 32 16 92 100 86 100 940 865 .464 2.154 2.619 2.276 2.157 1.781 52 323 2.06 .93 90 3000 8340 45 54 195 204 0 589 75 514 1.723 576 501 .58 2.095 .785 1.067 .785
12 599 781 127 89 472 692 601 834 129 92 474 745 0 0 209 307 31 24 98 100 96 100 1164 1219 .682 1.466 1.572 1.564 1.467 1.976 52 323 1.528 .94 90 3160 8330 44 53 211 220 0 625 71 554 1.173 667 596 .853 1.257 .23 .33 .23
13 381 394 128 90 253 304 403 428 132 96 275 338 0 0 124 146 30 29 93 93 93 90 557 613 .832 1.202 1.229 1.14 1.229 2.385 32 207 1.26 .89 70 3310 8330 45 52 227 234 0 315 72 243 .961 342 270 1.04 .983 -.057 -.024 -.057
14 207 188 128 96 79 92 197 193 133 97 69 97 0 0 58 45 30 22 80 92 53 86 171 166 .859 1.165 1.406 1.35 1.239 1.977 52 289 .886 .68 90 3450 8340 45 54 240 249 0 150 77 74 .932 154 78 1.073 1.125 -.102 .169 -.102
15 1842 2218 130 96 1712 2122 1929 2399 133 102 1799 2303 0 0 956 1041 32 58 100 100 96 100 3834 4102 .807 1.239 1.28 1.379 1.24 2.063 80 335 1.203 .96 100 3590 8340 45 55 254 264 0 1774 77 1698 .992 1919 1842 1.008 1.024 -.012 .034 -.012
16 858 1772 134 95 724 1677 915 2019 138 104 781 1924 0 0 238 538 39 67 98 100 98 100 2401 2705 .432 2.316 2.464 2.413 2.294 1.633 52 275 2.377 .97 90 3740 8330 44 53 269 278 0 1418 76 1342 1.853 1615 1539 .54 1.971 .89 .979 .89
17 166 99 133 89 33 10 155 98 136 89 22 9 0 0 50 17 30 14 45 35 28 15 43 31 3.3 .303 .409 .405 .369 2.86 80 405 .076 .18 100 3870 8320 43 53 282 292 -50 79 71 8 .242 78 7 4.125 .327 -1.611 -2.044
18 245 101 131 92 114 9 243 103 133 93 112 11 0 0 44 14 28 16 100 33 91 8 123 123 12.667 .079 .098 .111 .122 1.844 12 104 .099 .39 50 4040 8340 47 52 301 306 0 81 74 7 .063 82 9 15.833 .079 -3.985 -3.67 -3.985
19 356 412 127 96 229 316 308 324 130 97 181 228 0 0 159 237 28 14 92 96 88 94 545 409 .725 1.38 1.26 1.347 1.395 2.012 52 288 1.449 .9 90 4170 8340 45 54 312 321 0 330 77 253 1.104 259 182 .906 1.008 .143 .011 .143
20 205 106 126 98 79 8 217 106 129 98 91 8 0 0 57 20 28 14 82 40 69 17 87 99 9.875 .101 .088 .185 .183 2.914 52 243 .184 .51 80 4320 8330 45 53 328 336 0 85 78 6 .081 85 6 12.344 .07 -3.626 -3.83 -3.626

Total number of rows: 43008

Table truncated, full table size 9213 Kbytes.




Supplementary data files not provided

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