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Sample GSM95464 Query DataSets for GSM95464
Status Public on Feb 25, 2006
Title ES-2 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 Female vs ES-2 T80 CGH
Organism Homo sapiens
Characteristics Female vs ES-2 T80 CGH
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Drug_treatment, Taxol
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/36361.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
1 296 255 151 171 145 84 304 259 152 174 153 88 0 0 43 63 31 46 100 66 91 50 229 241 1.726 .579 .575 .472 .571 3.353 12 104 .99 .47 50 2020 7150 56 61 39 44 0 354 237 117 .804 359 122 1.244 .798 -.315 -.325
2 355 336 143 173 212 163 388 325 146 176 245 152 0 0 181 138 33 38 78 75 71 71 375 397 1.301 .769 .62 .829 .721 2.817 32 189 .757 .83 70 2160 7150 55 62 52 59 0 466 240 226 1.067 451 211 .937 .861 .093 -.216
3 168 199 145 175 23 24 152 177 148 173 7 2 0 0 65 96 31 41 26 25 9 13 47 9 .958 1.043 .286 1.475 1.571 3.434 52 230 1.486 .64 80 2280 7150 55 63 64 72 0 276 243 33 1.448 246 3 .691 .396 .534 -1.335
4 173 202 145 168 28 34 159 181 147 167 14 13 0 0 59 71 31 38 36 36 19 21 62 27 .824 1.214 .929 .907 1.119 4.923 52 278 .997 .6 80 2420 7150 55 63 78 86 0 280 233 47 1.685 251 18 .594 1.288 .753 .366
5 523 424 148 174 375 250 479 434 152 174 331 260 0 0 283 175 33 39 87 81 81 78 625 591 1.5 .667 .785 .65 .656 1.505 32 227 .638 .92 70 2590 7150 55 62 95 102 0 588 241 347 .925 602 361 1.081 1.09 -.112 .124
6 287 320 142 176 145 144 301 335 146 178 159 159 0 0 92 88 28 38 87 78 71 75 289 318 1.007 .993 1 .875 .953 2.48 32 225 .837 .77 70 2740 7150 55 62 110 117 0 444 244 200 1.378 465 221 .726 1.387 .462 .472
7 341 313 139 169 202 144 341 301 145 174 202 132 0 0 139 100 34 42 87 81 78 71 346 334 1.403 .713 .653 .801 .759 1.875 32 161 .702 .81 60 2890 7150 56 62 126 132 0 434 234 200 .989 418 183 1.011 .907 -.016 -.141
8 322 336 152 167 170 169 317 315 173 175 165 148 0 0 160 166 67 45 58 83 58 58 339 313 1.006 .994 .897 1.176 .935 2.273 12 80 .522 .8 50 3030 7130 54 59 140 145 0 466 232 234 1.379 437 205 .725 1.245 .464 .316
9 412 372 142 170 270 202 402 376 146 171 260 206 0 0 173 132 33 40 91 86 86 80 472 466 1.337 .748 .792 .761 .742 1.659 80 356 .742 .88 100 3150 7150 54 64 150 160 0 516 236 280 1.038 522 286 .963 1.099 .054 .137
10 215 223 146 168 69 55 204 236 155 175 58 68 0 0 61 64 39 42 65 56 37 34 124 126 1.255 .797 1.172 .986 .979 2.65 32 129 .941 .47 60 3280 7130 54 60 165 171 0 309 233 76 1.106 327 94 .904 1.627 .145 .702
11 399 343 146 170 253 173 411 338 155 178 265 168 0 0 117 95 51 49 94 94 88 78 426 433 1.462 .684 .634 .689 .654 1.848 52 325 .689 .85 90 3440 7140 53 62 179 188 0 476 236 240 .949 469 233 1.054 .88 -.076 -.185
12 297 327 141 172 156 155 292 313 150 178 151 141 0 0 53 53 45 49 98 100 88 86 311 292 1.006 .994 .934 1.002 .96 1.551 52 301 1.116 .78 90 3590 7150 54 63 194 203 0 454 239 215 1.379 434 196 .725 1.296 .463 .374
13 413 340 139 163 274 177 406 345 145 169 267 182 0 0 127 86 37 46 96 90 92 82 451 449 1.548 .646 .682 .673 .641 1.688 52 293 .664 .85 90 3730 7140 53 62 208 217 0 472 226 246 .896 479 253 1.116 .946 -.158 -.08
14 392 293 140 155 252 138 388 284 144 160 248 129 0 0 84 61 34 45 100 93 97 82 390 377 1.826 .548 .52 .533 .57 1.76 80 348 .605 .77 100 3890 7150 54 64 224 234 0 407 215 191 .76 394 179 1.316 .722 -.396 -.47
15 309 290 138 156 171 134 306 288 140 161 168 132 0 0 49 53 32 40 100 96 98 87 305 300 1.276 .784 .786 .723 .751 1.791 80 325 .873 .79 100 4030 7150 54 64 238 248 0 402 216 186 1.087 400 183 .92 1.09 .121 .125
16 142 171 143 159 -1 12 136 166 144 161 -7 7 0 0 47 64 32 38 11 21 3 7 11 0 null null null 1.472 1.348 3.999 52 225 1.536 .59 80 4180 7150 55 63 254 262 0 237 221 17 null 230 10 null null null null
17 736 465 144 156 592 309 811 501 148 157 667 345 0 0 301 164 42 39 93 91 92 86 901 1012 1.916 .522 .517 .528 .541 1.427 80 399 .542 .93 110 4320 7140 52 63 266 277 0 645 216 429 .724 695 479 1.381 .718 -.466 -.479
18 147 160 138 160 9 0 141 162 147 163 3 2 0 0 30 32 51 39 7 9 1 0 9 5 null null .667 1.267 1.462 4.826 52 186 .115 .04 80 4470 7150 55 63 283 291 0 222 222 0 null 225 3 null .925 null -.112
19 1507 1374 136 160 1371 1214 1593 1400 138 162 1457 1240 0 0 497 386 28 35 100 100 100 100 2585 2697 1.129 .885 .851 .915 .892 1.215 80 345 .863 .98 110 4610 7150 53 64 295 306 0 1906 222 1684 1.229 1942 1720 .814 1.181 .297 .24
20 589 513 138 149 451 364 630 528 140 151 492 379 0 0 176 128 31 36 100 98 100 98 815 871 1.239 .807 .77 .839 .798 1.527 80 305 .787 .93 100 4760 7150 54 64 311 321 0 712 207 505 1.12 733 526 .893 1.069 .163 .096

Total number of rows: 43104

Table truncated, full table size 9265 Kbytes.




Supplementary data files not provided
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