NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM95463 Query DataSets for GSM95463
Status Public on Feb 25, 2006
Title OVCAR3 CGH
Sample type genomic
 
Channel 1
Source name Female DNA
Organism Homo sapiens
Characteristics Female DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name OVCAR3 CGH
Organism Homo sapiens
Characteristics OVCAR3 CGH
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Drug_treatment, Taxol
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37109.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 Feb 03, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
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 GPL1448
Series (1)
GSE4173 Taxane-selected ovarian cancer cell lines

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
1 452 570 149 174 303 396 442 571 154 179 293 397 0 0 155 172 35 39 96 100 93 100 699 690 .765 1.307 1.355 1.375 1.255 1.402 32 162 1.289 .93 60 2100 7110 40 46 51 57 0 494 151 344 1.134 495 344 .882 1.175 .181 .233
2 877 868 153 173 724 695 882 871 157 176 729 698 0 0 363 329 38 42 96 100 96 100 1419 1427 1.042 .96 .957 1.001 .931 1.557 32 130 .947 .95 60 2240 7110 40 46 65 71 0 753 150 603 .833 756 606 1.201 .831 -.264 -.268
3 168 208 142 174 26 34 150 191 153 178 8 17 0 0 93 124 67 47 5 23 3 5 60 25 .765 1.308 2.125 1.707 1.369 4.354 52 240 1.019 .88 80 2350 7100 38 46 75 83 0 180 151 29 1.134 166 15 .881 1.843 .182 .882
4 445 413 142 178 303 235 292 337 144 180 150 159 0 0 286 222 29 41 78 71 75 62 538 309 1.289 .776 1.06 .833 .79 1.709 32 173 .775 .94 60 2530 7110 40 46 94 100 0 358 154 204 .673 292 138 1.486 .92 -.572 -.121
5 1215 1151 142 171 1073 980 1159 1214 143 176 1017 1043 0 0 719 589 29 43 96 93 90 90 2053 2060 1.095 .913 1.026 .934 .92 1.764 32 205 .881 .97 70 2670 7110 39 46 107 114 0 999 148 850 .792 1053 905 1.262 .89 -.336 -.169
6 626 755 144 177 482 578 582 794 148 179 438 617 0 0 339 371 29 41 90 90 84 84 1060 1055 .834 1.199 1.409 1.346 1.166 1.988 32 212 1.152 .97 70 2820 7110 39 46 122 129 0 655 154 501 1.04 689 535 .961 1.222 .057 .289
7 765 812 147 185 618 627 796 808 146 190 649 623 0 0 421 428 26 47 93 84 90 84 1245 1272 .986 1.015 .96 .911 .982 3.254 32 159 1.033 .97 60 2970 7100 39 45 138 144 0 704 160 544 .88 701 540 1.136 .833 -.184 -.264
8 913 1148 145 184 768 964 987 1185 145 187 842 1001 0 0 481 574 29 44 93 96 93 96 1732 1843 .797 1.255 1.189 1.492 1.31 1.887 32 167 1.239 .97 70 3100 7100 38 45 150 157 0 996 160 836 1.089 1028 868 .918 1.031 .123 .045
9 954 1255 143 193 811 1062 976 1292 146 191 833 1099 0 0 406 531 33 46 95 93 92 93 1873 1932 .764 1.309 1.319 1.334 1.298 1.422 80 284 1.323 .98 100 3220 7110 38 48 161 171 0 1089 167 921 1.136 1121 953 .88 1.145 .184 .195
10 453 431 145 197 308 234 363 409 154 202 218 212 0 0 503 234 52 63 90 80 80 73 542 430 1.316 .76 .972 .778 .897 2.093 52 212 .572 .95 80 3350 7100 38 46 175 183 0 374 171 203 .659 355 184 1.517 .844 -.601 -.245
11 875 1085 144 191 731 894 878 1141 150 198 734 950 0 0 363 407 42 58 93 96 93 95 1625 1684 .818 1.223 1.294 1.297 1.229 1.449 80 332 1.189 .97 100 3510 7110 38 48 190 200 0 941 166 776 1.061 990 824 .943 1.123 .085 .167
12 855 1141 141 183 714 958 829 1164 144 189 688 981 0 0 249 306 60 48 100 100 100 100 1672 1669 .745 1.342 1.426 1.353 1.323 1.229 80 304 1.328 .97 100 3670 7110 38 48 206 216 0 990 159 831 1.164 1010 851 .859 1.237 .219 .307
13 1130 1531 141 183 989 1348 1164 1597 141 186 1023 1414 0 0 432 490 30 47 100 100 100 100 2337 2437 .734 1.363 1.382 1.438 1.386 1.256 80 277 1.315 .98 100 3810 7110 38 48 220 230 0 1328 159 1169 1.182 1385 1227 .846 1.199 .242 .262
14 937 952 144 188 793 764 1029 1008 165 207 885 820 0 0 346 301 129 145 95 96 88 92 1557 1705 1.038 .963 .927 1.024 .96 1.559 80 325 1.013 .95 110 3950 7110 37 48 233 244 0 826 163 663 .836 874 711 1.196 .804 -.259 -.315
15 797 1236 145 192 652 1044 820 1255 178 227 675 1063 0 0 131 178 172 182 100 100 97 100 1696 1738 .625 1.601 1.575 1.614 1.594 1.271 80 350 1.596 .95 110 4100 7110 37 48 248 259 0 1072 167 906 1.389 1089 922 .72 1.366 .474 .45
16 166 218 143 179 23 39 144 189 148 195 1 10 0 0 85 159 55 81 13 15 5 5 62 11 .59 1.696 10 2.139 1.529 3.377 52 236 1.838 .86 80 4250 7100 38 46 265 273 0 189 155 34 1.471 164 9 .68 8.675 .557 3.117
17 1743 1446 145 184 1598 1262 1818 1524 195 226 1673 1340 0 0 607 433 210 178 96 94 90 92 2860 3013 1.266 .79 .801 .821 .81 1.229 52 299 .777 .98 90 4380 7100 37 46 277 286 0 1254 160 1095 .685 1322 1162 1.46 .695 -.546 -.525
18 140 192 144 195 -4 -3 143 185 205 239 -1 -10 0 0 29 52 225 183 0 0 0 0 -7 -11 null null null 2.474 3.042 2.895 52 238 .882 .78 80 4540 7100 38 46 294 302 0 167 169 -3 null 160 -9 null null null null
19 3823 5296 140 190 3683 5106 4131 5712 158 209 3991 5522 0 0 1730 2170 141 141 95 98 92 97 8789 9513 .721 1.386 1.384 1.477 1.41 1.265 80 335 1.362 .99 100 4680 7100 37 47 307 317 0 4594 165 4430 1.203 4955 4790 .831 1.2 .266 .263
20 1131 1048 138 183 993 865 1164 1068 176 215 1026 885 0 0 409 319 159 148 92 96 90 90 1858 1911 1.148 .871 .863 .918 .863 1.343 52 276 .866 .97 90 4820 7100 37 46 321 330 0 909 159 750 .756 927 768 1.323 .748 -.404 -.418

Total number of rows: 43104

Table truncated, full table size 9809 Kbytes.




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