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Sample GSM90021 Query DataSets for GSM90021
Status Public on Dec 30, 2005
Title PN92_2
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name PN92_2
Organism Homo sapiens
Characteristics PN92_2
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Prostate, Non-tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32177.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 Dec 29, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL3044
Series (1)
GSE3933 Prostate Cancer

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
1 363 139 196 71 167 68 376 126 200 77 180 55 0 0 106 71 57 37 78 59 71 36 235 235 2.456 .407 .306 .301 .297 4.127 52 274 .354 .52 80 1650 7720 88 96 69 77 0 151 77 74 .443 137 60 2.259 .332 -1.176 -1.59
2 332 101 184 72 148 29 323 102 191 76 139 30 0 0 85 28 60 33 84 46 65 9 177 169 5.103 .196 .216 .209 .274 2.903 52 243 .13 .37 80 1800 7720 88 96 84 92 0 110 78 32 .213 111 33 4.695 .235 -2.231 -2.092
3 2395 2150 187 75 2208 2075 2649 2377 219 98 2462 2302 0 0 822 849 208 150 98 98 95 96 4283 4764 1.064 .94 .935 .923 .975 1.408 80 411 .953 .96 110 1940 7710 85 96 96 107 0 2337 82 2255 1.021 2584 2502 .979 1.016 .031 .023
4 3143 5376 179 76 2964 5300 3191 5399 221 103 3012 5323 0 0 1340 2624 237 172 100 100 98 100 8264 8335 .559 1.788 1.767 1.782 1.845 1.371 52 305 1.883 .93 90 2100 7720 87 96 113 122 0 5843 83 5761 1.944 5868 5786 .515 1.921 .959 .942
5 425 452 172 71 253 381 431 508 182 78 259 437 0 0 124 240 52 48 93 93 84 81 634 696 .664 1.506 1.687 1.302 1.389 2.309 32 198 1.743 .84 70 2230 7710 87 94 127 134 0 491 77 414 1.637 552 475 .611 1.834 .711 .875
6 317 151 174 76 143 75 289 132 179 81 115 56 0 0 113 65 48 43 86 69 65 23 218 171 1.907 .524 .487 .487 .446 2.246 52 263 .452 .7 80 2380 7710 87 95 142 150 0 164 83 82 .57 143 61 1.754 .529 -.811 -.918
7 785 285 182 76 603 209 864 319 183 78 682 243 0 0 296 101 39 25 98 94 94 92 812 925 2.885 .347 .356 .346 .336 2.086 52 252 .309 .83 80 2530 7710 87 95 157 165 0 310 83 227 .377 347 264 2.654 .387 -1.408 -1.369
8 3527 3996 182 80 3345 3916 3465 4053 184 81 3283 3973 0 0 2694 2776 42 24 93 100 92 100 7261 7256 .854 1.171 1.21 1.523 1.194 2.698 80 347 1.116 .92 100 2670 7710 86 96 170 180 0 4343 87 4257 1.273 4405 4318 .786 1.315 .348 .396
9 669 887 179 82 490 805 620 796 187 82 441 714 0 0 379 663 91 24 88 100 76 100 1295 1155 .609 1.643 1.619 1.377 1.584 2.016 52 243 1.868 .78 80 2820 7700 86 94 186 194 0 964 89 875 1.786 865 776 .56 1.76 .837 .815
10 219 111 183 74 36 37 221 101 190 78 38 27 0 0 60 42 79 29 23 48 2 30 73 65 .973 1.028 .711 .744 .616 3.614 80 371 .451 .32 100 2960 7700 85 95 199 209 -50 121 80 40 1.117 110 29 .895 .772 .16 -.373
11 1951 1294 189 79 1762 1215 1996 1321 221 96 1807 1242 0 0 680 458 207 116 97 100 96 100 2977 3049 1.45 .69 .687 .715 .68 1.928 80 429 .667 .89 110 3110 7700 84 95 213 224 0 1407 86 1321 .75 1436 1350 1.334 .747 -.416 -.421
12 629 356 190 81 439 275 644 351 240 107 454 270 0 0 221 133 259 142 76 80 34 44 714 724 1.596 .626 .595 .686 .563 2.666 52 268 .511 .71 80 3260 7710 87 95 230 238 0 387 88 299 .681 382 293 1.469 .646 -.554 -.629
13 583 376 187 76 396 300 513 360 193 79 326 284 0 0 286 202 42 27 94 100 88 98 696 610 1.32 .758 .871 .861 .837 2.443 52 243 .654 .72 80 3410 7710 87 95 245 253 0 409 83 326 .823 391 309 1.214 .947 -.28 -.079
14 312 130 192 80 120 50 315 129 193 81 123 49 0 0 62 48 40 26 87 68 71 46 170 172 2.4 .417 .398 .551 .509 2.994 32 212 .286 .39 70 3550 7700 86 93 259 266 0 141 87 54 .453 140 53 2.208 .433 -1.143 -1.208
15 2251 1972 200 79 2051 1893 2208 2061 202 83 2008 1982 0 0 1496 1355 42 28 98 100 91 98 3944 3990 1.083 .923 .987 .965 .903 2.652 80 359 .861 .88 100 3700 7710 86 96 273 283 0 2143 86 2058 1.003 2240 2154 .997 1.073 .005 .101
16 1235 1106 200 77 1035 1029 1318 1178 203 80 1118 1101 0 0 540 557 40 24 96 100 94 98 2064 2219 1.006 .994 .985 1.064 1.012 1.985 52 293 1.071 .9 90 3840 7710 86 95 287 296 0 1202 84 1118 1.081 1280 1197 .925 1.07 .112 .098
17 289 210 200 78 89 132 289 213 201 82 89 135 0 0 61 63 40 23 76 96 55 88 221 224 .674 1.483 1.517 1.401 1.378 2.378 52 315 1.148 .57 90 3980 7700 85 94 301 310 0 228 85 143 1.612 232 147 .62 1.649 .689 .721
18 299 90 205 76 94 14 304 86 208 77 99 10 0 0 50 22 42 23 91 33 66 8 108 109 6.714 .149 .101 .254 .298 2.649 12 104 .093 .19 50 4120 7700 87 92 317 322 0 98 83 15 .162 93 11 6.177 .11 -2.627 -3.187
19 1078 946 185 76 893 870 1125 987 194 80 940 911 0 0 445 374 72 42 97 100 92 97 1763 1851 1.026 .974 .969 1.011 .917 1.813 80 449 .878 .9 110 4280 7700 84 95 330 341 0 1028 83 946 1.059 1073 990 .944 1.053 .083 .075
20 245 104 189 81 56 23 246 103 197 86 57 22 0 0 65 33 75 46 37 22 8 3 79 79 2.435 .411 .386 .453 .403 3.029 80 331 .7 .59 100 4420 7690 84 94 345 355 -50 113 88 25 .446 112 24 2.24 .42 -1.163 -1.253

Total number of rows: 43008

Table truncated, full table size 9087 Kbytes.




Supplementary data files not provided
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