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Sample GSM90042 Query DataSets for GSM90042
Status Public on Dec 30, 2005
Title PN191_6
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name PN191_6
Organism Homo sapiens
Characteristics PN191_6
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Prostate, Non-tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/29175.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
1 466 186 231 94 235 92 484 185 235 98 253 91 0 0 158 79 45 35 83 78 77 58 327 344 2.554 .391 .36 .441 .354 2.754 80 444 .315 .56 100 1840 8580 173 183 47 57 0 160 81 79 .337 159 78 2.963 .31 -1.567 -1.689
2 361 152 240 94 121 58 353 155 253 102 113 61 0 0 69 51 72 43 68 62 34 31 179 174 2.086 .479 .54 .505 .453 2.449 32 191 .392 .55 70 1960 8580 174 181 60 67 0 131 81 50 .413 134 53 2.42 .465 -1.275 -1.104
3 2128 1248 237 108 1891 1140 2360 1403 262 126 2123 1295 0 0 936 493 159 104 96 96 91 92 3031 3418 1.659 .603 .61 .628 .586 1.655 80 464 .577 .94 110 2120 8570 171 182 74 85 0 1076 93 983 .52 1209 1116 1.924 .526 -.944 -.927
4 4984 9240 239 103 4745 9137 4170 9842 265 125 3931 9739 0 0 3213 5610 179 116 96 100 92 100 13882 13670 .519 1.926 2.477 2.066 1.859 2.284 52 337 1.923 .93 90 2270 8580 173 182 90 99 0 7966 89 7877 1.66 8484 8396 .602 2.136 .731 1.095
5 626 388 239 95 387 293 664 384 242 102 425 289 0 0 235 183 45 42 90 100 81 81 680 714 1.321 .757 .68 .817 .718 1.991 32 213 .731 .81 70 2430 8580 174 181 107 114 0 334 82 253 .653 331 249 1.532 .586 -.616 -.771
6 395 202 241 101 154 101 395 199 245 105 154 98 0 0 92 67 56 40 86 82 71 59 255 252 1.525 .656 .636 .522 .66 3.027 52 286 .536 .5 80 2570 8580 174 182 121 129 0 174 87 87 .565 172 84 1.769 .549 -.823 -.866
7 1160 349 237 99 923 250 1311 368 243 103 1074 269 0 0 505 133 55 43 94 92 92 82 1173 1343 3.692 .271 .25 .293 .27 2.625 52 316 .237 .84 90 2720 8570 172 181 135 144 0 301 85 216 .233 317 232 4.283 .216 -2.099 -2.211
8 7215 6091 233 99 6982 5992 7502 6861 236 106 7269 6762 0 0 4168 3474 50 46 100 100 100 98 12974 14031 1.165 .858 .93 .834 .85 2.613 52 298 .845 .93 90 2850 8570 172 181 148 157 0 5251 85 5166 .74 5915 5829 1.352 .802 -.435 -.318
9 1304 807 235 111 1069 696 1475 861 235 112 1240 750 0 0 601 458 43 37 98 94 96 92 1765 1990 1.536 .651 .605 .61 .669 2.549 52 243 .638 .86 80 3010 8570 173 181 165 173 0 696 96 600 .561 742 647 1.782 .521 -.833 -.94
10 323 163 222 107 101 56 288 149 228 109 66 42 0 0 108 75 46 37 58 51 42 36 157 108 1.804 .554 .636 .584 .586 3.525 80 349 .545 .51 100 3140 8570 172 182 177 187 -50 141 92 48 .478 128 36 2.092 .549 -1.065 -.866
11 2773 2060 218 100 2555 1960 3126 2341 232 109 2908 2241 0 0 1023 791 97 71 100 100 100 100 4515 5149 1.304 .767 .771 .77 .731 1.647 80 407 .732 .93 110 3280 8570 171 182 190 201 0 1776 86 1690 .661 2018 1932 1.512 .664 -.597 -.59
12 1523 881 229 100 1294 781 1531 912 249 112 1302 812 0 0 863 532 127 83 88 92 82 84 2075 2114 1.657 .604 .624 .592 .597 2.708 52 235 .584 .93 80 3440 8570 173 181 208 216 0 759 86 673 .52 786 700 1.922 .538 -.943 -.895
13 1118 897 227 98 891 799 1174 968 231 102 947 870 0 0 533 483 58 40 94 100 92 96 1690 1817 1.115 .897 .919 .94 .938 1.95 52 264 .872 .92 80 3580 8570 173 181 222 230 0 773 84 689 .773 834 750 1.294 .792 -.371 -.336
14 417 335 234 106 183 229 420 326 236 114 186 220 0 0 120 91 49 60 81 96 78 87 412 406 .799 1.251 1.183 1.296 1.175 2.149 32 158 1.076 .72 60 3740 8570 174 180 239 245 0 289 91 197 1.079 281 190 .927 1.02 .109 .028
15 5013 4118 223 101 4790 4017 5226 4493 228 113 5003 4392 0 0 2942 2691 47 97 100 100 98 95 8807 9395 1.192 .839 .878 .828 .832 1.986 80 359 .855 .94 100 3880 8580 173 183 251 261 0 3550 87 3463 .723 3873 3786 1.383 .757 -.468 -.402
16 2047 2504 214 93 1833 2411 2299 2830 218 98 2085 2737 0 0 1057 1254 41 39 96 100 96 97 4244 4822 .76 1.315 1.313 1.47 1.309 2.394 80 383 1.305 .92 100 4010 8580 173 183 264 274 0 2159 80 2078 1.134 2440 2359 .882 1.132 .181 .178
17 333 285 215 106 118 179 337 277 219 112 122 171 0 0 56 86 42 47 90 93 78 81 297 293 .659 1.517 1.402 1.478 1.577 2.033 32 210 1.808 .6 70 4180 8560 172 179 282 289 0 246 91 154 1.308 239 147 .765 1.208 .387 .273
18 330 179 220 101 110 78 331 158 234 108 111 57 0 0 66 78 170 46 21 59 0 32 188 168 1.41 .709 .514 .619 .532 3.396 52 226 .743 .42 80 4310 8570 173 181 295 303 0 154 87 67 .611 136 49 1.636 .443 -.71 -1.176
19 1612 2450 218 106 1394 2344 1717 2424 234 115 1499 2318 0 0 527 824 132 52 100 100 96 100 3738 3817 .595 1.681 1.546 1.751 1.667 1.491 80 451 1.687 .92 110 4440 8570 171 182 306 317 0 2112 91 2021 1.45 2090 1998 .69 1.333 .536 .415
20 401 235 235 119 166 116 373 208 248 122 138 89 0 0 108 96 68 43 83 66 58 50 282 227 1.431 .699 .645 .612 .594 7.023 12 92 .481 .19 50 4610 8570 174 179 326 331 0 203 103 100 .602 179 77 1.66 .556 -.731 -.847

Total number of rows: 43008

Table truncated, full table size 9257 Kbytes.




Supplementary data files not provided
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