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Sample GSM95456 Query DataSets for GSM95456
Status Public on Feb 25, 2006
Title OVCAR3 TxT5 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 TxT5 CGH
Organism Homo sapiens
Characteristics OVCAR3 TxT5 CGH
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Drug_treatment, Taxol
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37390.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
1 752 797 271 221 481 576 755 783 279 218 484 562 0 0 117 140 73 55 100 100 100 100 1057 1046 .835 1.198 1.161 1.195 1.191 1.322 32 186 1.195 .9 70 2180 7100 50 57 70 77 0 735 204 531 1.104 722 518 .906 1.071 .143 .098
2 1224 1019 265 216 959 803 1224 1017 272 210 959 801 0 0 303 253 59 53 100 100 100 100 1762 1760 1.194 .837 .835 .845 .83 1.348 52 257 .839 .94 80 2320 7090 49 57 84 92 0 940 199 740 .772 938 739 1.295 .77 -.373 -.377
3 831 661 242 217 589 444 804 696 250 216 562 479 0 0 248 170 47 49 100 100 100 100 1033 1041 1.327 .754 .852 .765 .812 1.552 32 158 .746 .87 60 2470 7090 50 56 100 106 0 609 200 409 .695 642 442 1.439 .786 -.525 -.348
4 742 587 233 211 509 376 708 579 231 218 475 368 0 0 203 168 47 52 100 100 100 93 885 843 1.354 .739 .775 .713 .699 1.696 32 155 .721 .84 60 2610 7080 49 55 114 120 0 541 195 347 .681 534 339 1.468 .714 -.554 -.485
5 1419 1189 215 205 1204 984 1434 1253 217 210 1219 1048 0 0 485 362 58 52 100 100 100 100 2188 2267 1.224 .817 .86 .855 .802 1.505 52 297 .772 .92 90 2750 7090 48 57 126 135 0 1096 189 907 .754 1155 966 1.327 .793 -.408 -.335
6 1073 1061 207 204 866 857 1043 986 206 210 836 782 0 0 376 350 42 56 100 100 100 100 1723 1618 1.011 .99 .935 .996 .972 1.453 52 227 .984 .91 80 2900 7090 49 57 142 150 0 978 188 790 .912 909 721 1.096 .862 -.132 -.213
7 1001 872 202 209 799 663 970 887 201 210 768 678 0 0 277 256 37 49 100 98 100 98 1462 1446 1.205 .83 .883 .812 .839 1.415 52 233 .83 .94 80 3050 7090 49 57 157 165 0 804 193 611 .765 818 625 1.307 .814 -.386 -.297
8 746 852 203 211 543 641 696 769 202 212 493 558 0 0 360 407 38 53 94 92 88 88 1184 1051 .847 1.18 1.132 1.125 1.136 1.646 52 235 1.158 .91 80 3190 7090 49 57 171 179 0 786 195 591 1.088 709 515 .919 1.044 .122 .062
9 1172 1220 192 208 980 1012 1173 1233 195 211 981 1025 0 0 284 299 41 56 100 100 100 100 1992 2006 .968 1.033 1.045 1.027 1.051 1.279 80 366 1.044 .95 110 3350 7090 47 58 185 196 0 1125 192 933 .952 1137 945 1.05 .963 -.071 -.054
10 548 566 187 222 361 344 529 561 192 228 342 339 0 0 145 130 40 70 100 98 98 94 705 681 1.049 .953 .991 .958 .951 1.752 52 258 1.003 .82 90 3500 7080 47 56 201 210 0 522 205 317 .879 517 313 1.138 .914 -.187 -.13
11 1001 1090 184 214 817 876 982 1074 189 220 798 860 0 0 201 238 39 66 100 100 100 100 1693 1658 .933 1.072 1.078 1.065 1.079 1.272 80 311 1.087 .95 100 3640 7090 48 58 215 225 0 1005 197 808 .989 990 793 1.011 .994 -.016 -.009
12 779 814 173 209 606 605 804 765 180 213 631 556 0 0 216 230 38 53 100 98 100 98 1211 1187 1.002 .998 .881 .986 .991 1.353 80 290 1.027 .93 100 3790 7090 48 58 230 240 0 751 193 558 .921 705 513 1.086 .812 -.119 -.3
13 1111 1323 174 195 937 1128 1131 1347 177 200 957 1152 0 0 298 390 37 51 100 100 100 100 2065 2109 .831 1.204 1.204 1.187 1.19 1.291 80 280 1.225 .95 100 3940 7080 47 57 245 255 0 1220 180 1040 1.11 1242 1062 .901 1.11 .151 .15
14 1076 1003 176 186 900 817 1098 1016 176 190 922 830 0 0 255 242 34 49 100 100 100 100 1717 1752 1.102 .908 .9 .904 .911 1.279 80 320 .919 .95 110 4080 7080 46 57 258 269 0 925 172 753 .837 937 765 1.195 .83 -.257 -.269
15 763 1051 176 200 587 851 759 1084 177 211 583 884 0 0 114 187 35 82 100 100 100 100 1438 1467 .69 1.45 1.516 1.438 1.451 1.275 80 357 1.496 .94 110 4220 7090 47 58 272 283 0 969 184 785 1.337 999 815 .748 1.398 .419 .483
16 268 252 178 197 90 55 199 211 184 201 21 14 0 0 278 181 35 54 38 23 19 15 145 35 1.636 .611 .667 1.046 .97 3.145 52 230 .652 .74 80 4370 7090 49 57 289 297 0 232 182 51 .563 195 13 1.775 .615 -.828 -.702
17 2036 1682 184 193 1852 1489 2073 1696 188 198 1889 1503 0 0 545 378 41 51 100 100 100 100 3341 3392 1.244 .804 .796 .819 .843 1.214 80 364 .792 .97 110 4520 7090 47 58 302 313 0 1551 178 1373 .741 1564 1386 1.349 .734 -.432 -.447
18 246 302 184 196 62 106 193 203 185 198 9 7 0 0 159 249 40 52 26 34 17 25 168 16 .585 1.71 .778 1.705 1.826 4.059 52 206 1.396 .84 80 4670 7090 49 57 319 327 0 278 181 98 1.576 187 6 .634 .717 .657 -.48
19 4297 5148 182 190 4115 4958 4612 5400 182 192 4430 5210 0 0 1613 1758 39 49 100 100 100 100 9073 9640 .83 1.205 1.176 1.226 1.191 1.206 80 347 1.189 .98 110 4820 7090 47 58 332 343 0 4747 175 4572 1.111 4979 4804 .9 1.084 .152 .117
20 2470 2645 184 185 2286 2460 2530 2626 187 186 2346 2441 0 0 817 910 46 46 100 100 100 100 4746 4787 .929 1.076 1.04 1.063 1.092 1.273 80 277 1.085 .97 100 4960 7080 47 57 347 357 0 2439 171 2268 .992 2421 2251 1.008 .959 -.011 -.06

Total number of rows: 43104

Table truncated, full table size 9994 Kbytes.




Supplementary data files not provided
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