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Sample GSM95438 Query DataSets for GSM95438
Status Public on Feb 25, 2006
Title 1A9 T80 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 1A9 T80 CGH
Organism Homo sapiens
Characteristics 1A9 T80 CGH
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Drug_treatment, Taxol
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37112.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
1 355 272 212 184 143 88 348 282 213 178 136 98 0 0 69 76 39 45 100 68 78 56 231 234 1.625 .615 .721 .633 .575 2.37 32 157 .708 .53 60 2070 7130 30 36 52 58 0 323 219 105 .732 335 117 1.366 .857 -.45 -.223
2 460 372 192 183 268 189 439 358 192 181 247 175 0 0 163 119 40 52 93 81 87 71 457 422 1.418 .705 .709 .635 .619 1.809 32 141 .689 .82 60 2210 7120 29 35 66 72 0 442 218 225 .839 426 208 1.192 .843 -.254 -.247
3 192 187 172 173 20 14 166 178 176 174 -6 5 0 0 83 59 36 48 21 25 11 9 34 -1 1.429 .7 null 1.102 1.107 4.787 52 251 .793 .46 80 2330 7120 28 36 77 85 0 222 206 17 .833 212 6 1.201 null -.264 null
4 315 244 169 178 146 66 322 234 178 182 153 56 0 0 90 69 49 50 83 50 66 33 212 209 2.212 .452 .366 .59 .515 4.486 12 98 .61 .72 50 2500 7110 28 33 95 100 0 290 212 78 .538 278 67 1.86 .435 -.895 -1.2
5 646 435 173 172 473 263 579 421 174 176 406 249 0 0 286 185 30 48 100 87 100 81 736 655 1.798 .556 .613 .517 .626 1.96 32 221 .567 .86 70 2650 7120 28 35 109 116 0 517 205 313 .661 501 296 1.512 .729 -.597 -.455
6 357 282 183 172 174 110 345 287 183 182 162 115 0 0 100 90 34 54 90 65 81 53 284 277 1.582 .632 .71 .544 .579 2.792 32 163 .757 .6 60 2800 7120 29 35 125 131 0 335 205 131 .752 341 137 1.33 .844 -.411 -.244
7 391 328 171 175 220 153 374 332 175 177 203 157 0 0 171 140 36 49 84 75 75 65 373 360 1.438 .695 .773 .893 .753 2.878 32 161 .756 .79 60 2940 7120 29 35 139 145 0 390 208 182 .827 395 187 1.209 .92 -.274 -.121
8 469 313 174 182 295 131 496 345 187 192 322 163 0 0 212 150 60 65 75 66 66 58 426 485 2.252 .444 .506 .513 .497 1.443 12 90 .619 .8 50 3070 7100 27 32 152 157 0 372 216 156 .528 410 194 1.893 .602 -.921 -.732
9 509 364 172 170 337 194 505 332 180 182 333 162 0 0 141 116 50 63 96 90 92 67 531 495 1.737 .576 .486 .529 .554 1.906 52 299 .645 .81 90 3200 7110 26 35 163 172 0 433 202 231 .685 395 193 1.461 .579 -.547 -.789
10 268 250 166 172 102 78 268 247 174 180 102 75 0 0 59 68 43 49 88 61 65 38 180 177 1.308 .765 .735 .665 .873 3.264 52 213 1.043 .44 80 3340 7110 27 35 178 186 0 297 205 93 .909 294 89 1.1 .874 -.137 -.193
11 476 343 181 175 295 168 506 340 188 181 325 165 0 0 127 90 55 56 94 88 90 69 463 490 1.756 .569 .508 .539 .576 2.061 52 299 .557 .8 90 3480 7110 26 35 191 200 0 408 208 200 .677 404 196 1.476 .604 -.562 -.728
12 426 382 174 177 252 205 411 374 179 183 237 197 0 0 91 106 52 55 98 96 98 76 457 434 1.229 .813 .831 .717 .79 1.979 52 294 .861 .75 90 3640 7120 27 36 207 216 0 454 211 244 .967 445 234 1.034 .989 -.048 -.017
13 556 473 168 165 388 308 557 496 167 171 389 331 0 0 163 129 34 47 100 98 100 92 696 720 1.26 .794 .851 .772 .772 1.449 52 263 .787 .88 90 3780 7120 27 36 221 230 0 563 196 366 .944 590 394 1.059 1.012 -.083 .017
14 488 372 166 154 322 218 505 374 167 160 339 220 0 0 131 100 37 45 96 93 92 91 540 559 1.477 .677 .649 .673 .649 1.527 80 318 .708 .84 100 3930 7110 26 36 236 246 0 442 183 259 .805 445 262 1.242 .772 -.313 -.374
15 401 396 165 170 236 226 397 413 178 178 232 243 0 0 111 119 69 60 91 86 86 81 462 475 1.044 .958 1.047 .988 1.011 2.039 80 378 .999 .79 110 4070 7110 25 36 249 260 0 471 202 269 1.139 491 289 .878 1.246 .188 .317
16 173 170 164 172 9 -2 165 163 178 179 1 -9 0 0 34 54 72 64 5 11 0 1 7 -8 null null null 1.703 1.545 3.412 52 232 4.173 .14 80 4230 7110 27 35 267 275 0 202 205 -2 null 194 -11 null null null null
17 747 501 162 158 585 343 809 493 173 166 647 335 0 0 312 212 64 57 87 88 85 83 928 982 1.706 .586 .518 .557 .577 1.757 80 328 .597 .91 100 4360 7110 26 36 279 289 0 596 188 408 .697 586 398 1.434 .616 -.52 -.699
18 173 191 173 165 0 26 172 183 184 172 -1 18 0 0 42 51 73 57 3 26 1 5 26 17 null null null 2.261 2.124 3.926 52 211 1.797 .26 80 4520 7110 27 35 296 304 0 227 196 31 null 218 21 null null null null
19 1730 1514 169 168 1561 1346 1840 1504 174 178 1671 1336 0 0 874 787 49 75 95 91 91 86 2907 3007 1.16 .862 .8 .82 .839 1.511 80 323 .88 .96 100 4650 7110 26 36 308 318 0 1801 200 1601 1.025 1789 1589 .975 .951 .036 -.073
20 725 980 167 166 558 814 805 1025 173 177 638 859 0 0 309 563 56 81 86 86 86 80 1372 1497 .686 1.459 1.346 1.25 1.389 1.686 80 315 1.627 .92 100 4800 7110 26 36 323 333 0 1166 197 968 1.735 1219 1022 .576 1.601 .795 .679

Total number of rows: 43104

Table truncated, full table size 9380 Kbytes.




Supplementary data files not provided
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