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Sample GSM90058 Query DataSets for GSM90058
Status Public on Dec 30, 2005
Title PT318_2
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name PT318_2
Organism Homo sapiens
Characteristics PT318_2
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Prostate, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-01/24163.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
1 237 133 95 52 142 81 212 127 98 55 117 75 0 0 144 72 23 18 71 76 67 66 223 192 1.753 .57 .641 .567 .526 3.185 80 407 .419 .65 100 1770 8780 113 123 88 98 0 106 41 64 .453 101 60 2.209 .509 -1.143 -.975
2 224 106 92 49 132 57 241 108 95 51 149 59 0 0 90 40 22 18 85 81 81 63 189 208 2.316 .432 .396 .422 .442 2.267 80 306 .334 .66 100 1910 8780 113 123 102 112 0 84 39 45 .343 86 47 2.918 .314 -1.545 -1.67
3 1027 846 92 54 935 792 1109 914 96 56 1017 860 0 0 524 416 24 18 91 100 90 99 1727 1877 1.181 .847 .846 .842 .848 2.885 120 498 .8 .81 120 2060 8780 112 124 116 128 0 671 43 629 .672 725 683 1.488 .671 -.573 -.575
4 2157 4463 94 53 2063 4410 2022 3430 97 55 1928 3377 0 0 1567 3466 25 18 88 100 88 100 6473 5305 .468 2.138 1.752 1.661 2.025 4.494 52 291 2.694 .74 90 2220 8780 113 122 133 142 0 3542 42 3500 1.697 2722 2680 .589 1.39 .763 .475
5 258 268 97 53 161 215 216 199 100 54 119 146 0 0 167 195 28 17 67 87 62 76 376 265 .749 1.335 1.227 .957 1.227 4.318 80 343 1.372 .62 100 2370 8780 113 123 148 158 0 213 42 171 1.06 158 116 .944 .974 .084 -.038
6 208 123 97 53 111 70 236 126 104 56 139 73 0 0 97 39 49 21 69 84 59 75 181 212 1.586 .631 .525 .585 .446 3.452 52 318 .367 .53 90 2500 8780 113 122 161 170 0 98 42 56 .501 100 58 1.998 .417 -.999 -1.263
7 399 157 94 51 305 106 470 165 101 55 376 114 0 0 214 64 51 21 78 80 73 76 411 490 2.877 .348 .303 .318 .286 3.049 52 293 .273 .74 90 2660 8770 112 121 177 186 0 125 40 84 .276 131 90 3.625 .241 -1.858 -2.055
8 1967 2968 94 54 1873 2914 2181 3154 96 57 2087 3100 0 0 1307 1686 24 19 95 100 91 100 4787 5187 .643 1.556 1.485 1.705 1.381 3.688 80 294 1.555 .79 100 2790 8780 113 123 190 200 0 2356 43 2313 1.235 2503 2460 .81 1.179 .304 .237
9 464 567 95 54 369 513 408 545 99 57 313 491 0 0 328 336 25 19 78 95 71 93 882 804 .719 1.39 1.569 1.256 1.156 3.388 80 349 1.294 .74 100 2940 8780 113 123 205 215 0 450 43 407 1.103 433 390 .906 1.245 .142 .316
10 329 315 111 65 218 250 349 294 121 84 238 229 0 0 96 144 58 70 100 83 75 83 468 467 .872 1.147 .962 .96 1.105 2.75 12 99 1.225 .54 50 3070 8770 114 119 220 225 0 250 52 198 .91 233 182 1.099 .764 -.136 -.389
11 1077 951 103 62 974 889 1221 1074 166 85 1118 1012 0 0 489 411 577 129 76 95 43 85 1863 2130 1.096 .913 .905 .973 .875 2.946 80 497 .877 .86 110 3210 8770 111 122 231 242 0 755 49 706 .724 852 803 1.38 .718 -.465 -.477
12 561 502 97 58 464 444 476 471 118 74 379 413 0 0 411 322 95 87 69 80 67 69 908 792 1.045 .957 1.09 .75 .759 3.952 52 261 .862 .8 80 3380 8770 113 121 250 258 0 398 46 352 .759 374 328 1.317 .865 -.397 -.209
13 375 330 96 55 279 275 397 294 101 65 301 239 0 0 229 183 34 45 75 87 71 83 554 540 1.015 .986 .794 .772 .817 2.939 80 371 .871 .8 100 3530 8780 113 123 264 274 0 262 44 218 .782 233 190 1.278 .63 -.354 -.666
14 239 247 99 58 140 189 263 257 106 72 164 199 0 0 107 100 40 52 81 90 81 75 329 363 .741 1.35 1.213 1.06 1.027 2.19 32 191 1.222 .69 70 3690 8770 113 120 281 288 0 196 46 150 1.071 204 158 .933 .963 .1 -.054
15 1727 1806 97 60 1630 1746 1556 1776 105 89 1459 1716 0 0 1247 1194 44 184 88 91 85 80 3376 3175 .934 1.071 1.176 1.112 .953 2.864 80 348 1.022 .84 100 3810 8780 113 123 292 302 0 1433 48 1386 .85 1410 1362 1.176 .933 -.234 -.099
16 957 1164 98 58 859 1106 1007 1326 101 62 909 1268 0 0 546 682 26 29 86 100 86 97 1965 2177 .777 1.288 1.395 1.15 1.237 2.7 80 415 1.335 .89 110 3950 8770 111 122 305 316 0 924 46 878 1.022 1052 1006 .979 1.107 .031 .147
17 190 189 98 59 92 130 196 205 107 68 98 146 0 0 108 82 42 35 68 81 56 71 222 244 .708 1.413 1.49 1.047 1.027 2.209 32 176 .979 .7 60 4120 8770 114 120 325 331 0 150 47 103 1.121 163 116 .892 1.182 .165 .242
18 235 107 117 68 118 39 241 91 135 82 124 23 0 0 44 43 61 67 91 8 50 8 157 147 3.026 .331 .185 .295 .243 2.157 12 86 .284 .35 50 4270 8760 113 118 340 345 0 85 54 31 .262 72 18 3.812 .147 -1.931 -2.764
19 616 1047 104 58 512 989 724 1141 106 65 620 1083 0 0 254 531 29 48 91 98 90 95 1501 1703 .518 1.932 1.747 1.833 1.868 2.585 80 427 2.166 .84 110 4390 8760 110 121 349 360 0 831 46 785 1.533 906 860 .652 1.386 .616 .471
20 154 92 105 58 49 34 145 79 106 71 40 21 0 0 77 46 29 114 53 6 43 0 83 61 1.441 .694 .525 .494 .511 2.706 80 376 .502 .47 100 4540 8760 111 121 365 375 -50 73 46 27 .551 63 17 1.816 .417 -.861 -1.263

Total number of rows: 43008

Table truncated, full table size 9089 Kbytes.




Supplementary data files not provided
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