NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM90106 Query DataSets for GSM90106
Status Public on Dec 30, 2005
Title PT110_2
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name PT110_2
Organism Homo sapiens
Characteristics PT110_2
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Prostate, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32277.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
1 328 167 150 100 178 67 339 162 156 105 189 62 0 0 104 68 39 40 86 67 84 32 245 251 2.657 .376 .328 .42 .367 5.412 52 337 .273 .33 90 1700 8000 51 60 65 74 0 232 139 93 .523 225 86 1.913 .456 -.936 -1.134
2 392 217 173 110 219 107 413 204 923 326 240 94 0 0 118 80 5346 1706 0 0 0 0 326 334 2.047 .489 .392 .492 .431 3.894 32 198 .239 .38 70 1850 8000 52 59 81 88 0 301 153 149 .679 283 131 1.474 .544 -.559 -.878
3 2876 2431 155 98 2721 2333 3222 2685 183 118 3067 2587 0 0 1178 934 219 151 96 100 91 93 5054 5654 1.166 .857 .843 .903 .87 1.473 80 480 .821 .95 110 1990 7990 49 60 93 104 0 3376 136 3240 1.191 3729 3593 .84 1.172 .252 .228
4 4445 3846 157 102 4288 3744 4189 3710 200 129 4032 3608 0 0 3141 2678 272 186 92 98 92 98 8032 7640 1.145 .873 .895 .927 .884 1.65 52 305 .856 .95 90 2140 8000 51 60 109 118 0 5342 142 5200 1.213 5153 5011 .825 1.243 .278 .314
5 505 421 153 97 352 324 487 386 157 103 334 289 0 0 224 184 34 40 92 100 86 96 676 623 1.086 .92 .865 .967 .83 2.225 52 251 .87 .85 80 2280 8000 52 60 124 132 0 585 135 450 1.278 536 401 .782 1.202 .354 .265
6 351 220 153 89 198 131 362 211 155 94 209 122 0 0 93 83 34 37 98 86 92 75 329 331 1.511 .662 .584 .593 .579 2.664 52 275 .589 .55 80 2440 8000 52 60 140 148 0 306 124 182 .919 293 169 1.088 .811 -.122 -.303
7 1065 626 157 97 908 529 1231 704 158 102 1074 607 0 0 496 231 33 38 98 100 96 98 1437 1681 1.716 .583 .565 .705 .566 2.338 52 325 .51 .9 90 2580 7990 50 59 153 162 0 869 135 735 .809 978 843 1.236 .785 -.305 -.349
8 6856 7917 157 98 6699 7819 7018 8788 161 103 6861 8690 0 0 4348 4793 36 38 100 100 100 100 14518 15551 .857 1.167 1.267 1.267 1.126 2.099 52 326 1.134 .95 90 2730 7990 50 59 168 177 0 10996 136 10860 1.621 12206 12069 .617 1.759 .697 .815
9 1048 991 157 99 891 892 1002 897 160 109 845 798 0 0 570 646 38 70 94 98 92 96 1783 1643 .999 1.001 .944 .96 .983 2.119 52 329 1.054 .92 90 2870 8000 51 60 182 191 0 1376 138 1239 1.39 1246 1108 .719 1.312 .476 .391
10 288 224 164 114 124 110 292 227 172 142 128 113 0 0 66 77 58 105 81 53 56 6 234 241 1.127 .887 .883 .8 .912 3.065 32 158 1.023 .36 60 3020 8000 53 59 199 205 0 311 158 153 1.232 315 157 .812 1.226 .301 .294
11 2306 1185 162 107 2144 1078 2487 1241 194 135 2325 1134 0 0 913 420 186 136 96 98 95 92 3222 3459 1.989 .503 .488 .538 .503 1.709 80 479 .478 .94 110 3160 7990 49 60 210 221 0 1646 149 1497 .698 1724 1575 1.432 .677 -.518 -.562
12 701 383 168 102 533 281 731 380 226 137 563 278 0 0 257 123 268 157 78 81 50 37 814 841 1.897 .527 .494 .541 .584 1.861 32 204 .493 .85 70 3300 8000 52 59 226 233 0 532 142 390 .732 528 386 1.366 .686 -.45 -.544
13 687 339 158 101 529 238 644 316 165 111 486 215 0 0 384 119 41 63 90 96 88 86 767 701 2.223 .45 .442 .489 .42 2.528 52 260 .336 .75 80 3460 8000 52 60 242 250 0 471 140 331 .625 439 299 1.6 .614 -.678 -.703
14 314 225 160 101 154 124 314 215 165 107 154 114 0 0 106 86 38 42 78 81 75 59 278 268 1.242 .805 .74 .859 .775 2.692 32 164 .721 .51 60 3600 8000 53 59 257 263 0 313 140 172 1.118 299 158 .894 1.028 .161 .04
15 2696 1703 160 104 2536 1599 2886 1942 163 116 2726 1838 0 0 1748 1066 38 78 93 95 93 93 4135 4564 1.586 .631 .674 .74 .638 2.597 80 394 .598 .92 100 3750 8000 51 61 270 280 0 2365 144 2221 .876 2697 2553 1.142 .936 -.191 -.095
16 1413 810 159 105 1254 705 1520 804 161 114 1361 699 0 0 877 468 37 79 93 92 90 83 1959 2060 1.779 .562 .514 .606 .538 2.152 80 355 .524 .9 100 3890 8000 51 61 284 294 0 1125 146 979 .781 1117 971 1.281 .713 -.357 -.487
17 258 244 155 104 103 140 272 236 155 107 117 132 0 0 82 86 37 39 75 88 63 75 243 249 .736 1.359 1.128 1.229 1.106 2.975 52 313 1.304 .58 90 4030 7990 50 59 298 307 0 339 144 194 1.888 328 183 .53 1.567 .917 .648
18 286 144 157 98 129 46 303 131 160 102 146 33 0 0 91 66 37 37 81 46 71 25 175 179 2.804 .357 .226 .544 .519 3.807 32 207 .213 .11 70 4180 8000 52 59 314 321 0 200 136 64 .495 182 46 2.019 .314 -1.014 -1.671
19 1053 724 155 95 898 629 1059 719 161 103 904 624 0 0 424 277 64 46 97 100 96 96 1527 1528 1.428 .7 .69 .739 .734 1.717 80 479 .652 .9 110 4330 7990 49 60 327 338 0 1006 132 874 .973 999 867 1.028 .959 -.04 -.061
20 303 168 159 105 144 63 332 164 173 114 173 59 0 0 93 72 82 59 81 50 53 21 207 232 2.286 .438 .341 .531 .505 2.511 32 213 .434 .38 70 4470 8010 53 60 343 350 0 233 146 88 .608 228 82 1.646 .474 -.719 -1.078

Total number of rows: 43008

Table truncated, full table size 9072 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap