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Sample GSM95459 Query DataSets for GSM95459
Status Public on Feb 25, 2006
Title OV429 T80
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Characteristics CRH
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name CRH vs OV429 T80
Organism Homo sapiens
Characteristics CRH vs OV429 T80
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Drug_treatment, Taxol
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29751.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 GPL2696
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
1 569 1013 144 139 425 874 582 1046 176 156 438 907 0 0 150 167 291 152 84 100 11 100 1299 1345 .486 2.056 2.071 2.235 2.109 1.636 52 286 2.024 .67 80 1570 8990 39 47 37 45 0 974 134 840 1.977 1006 872 .506 1.991 .984 .994
2 70 48 67 51 3 -3 64 46 82 68 -3 -5 0 0 22 17 46 53 5 0 0 0 0 -8 null null null .694 .739 3.336 52 256 .841 .59 80 1710 8980 38 46 51 59 0 46 49 -3 null 44 null null null null null
3 67 58 58 51 9 7 62 42 63 55 4 -9 0 0 20 87 24 23 21 7 5 3 16 -5 1.286 .778 null 1.122 .917 3.57 52 256 .683 .21 80 1860 8980 38 46 66 74 0 56 49 7 .748 40 null 1.337 null -.419 null
4 60 49 60 49 0 0 56 46 67 57 -4 -3 0 0 19 21 29 30 5 9 0 0 0 -7 null null null .965 .916 3.462 52 278 .658 .04 80 2000 8980 38 46 80 88 0 47 47 0 null 44 null null null null null
5 363 249 107 125 256 124 223 193 116 128 116 68 0 0 321 218 62 79 53 46 48 34 380 184 2.065 .484 .586 .847 .918 3.426 52 278 .617 .64 80 2150 8980 38 46 95 103 0 239 120 119 .466 186 65 2.147 .564 -1.102 -.827
6 319 596 149 166 170 430 304 599 149 174 155 433 0 0 78 160 46 62 100 100 83 100 600 588 .395 2.529 2.794 2.599 2.91 1.999 12 104 2.858 .7 50 2290 8980 39 44 110 115 0 573 160 413 2.432 576 416 .411 2.686 1.282 1.426
7 1588 645 145 158 1443 487 1602 637 155 168 1457 479 0 0 304 227 67 72 100 96 100 94 1930 1936 2.963 .337 .329 .292 .334 1.849 52 335 .317 .54 90 2440 8980 37 46 123 132 0 620 152 468 .325 613 461 3.082 .316 -1.624 -1.661
8 4279 6197 146 169 4133 6028 4868 6222 163 184 4722 6053 0 0 2554 3873 92 79 95 100 95 100 10161 10775 .686 1.459 1.282 1.522 1.484 2.135 80 419 1.526 .94 110 2590 8990 37 48 137 148 0 5959 163 5796 1.402 5983 5820 .713 1.233 .488 .302
9 957 1781 143 179 814 1602 903 1538 157 195 760 1359 0 0 399 1426 62 100 100 100 98 100 2416 2119 .508 1.968 1.788 1.842 1.756 1.722 52 319 3.019 .73 90 2730 8980 37 46 152 161 0 1713 172 1540 1.892 1479 1307 .528 1.719 .92 .782
10 365 346 148 163 217 183 358 336 155 174 210 173 0 0 108 98 56 87 93 84 84 46 400 383 1.186 .843 .824 .811 .757 2.059 32 198 .848 .69 70 2870 8990 39 46 167 174 0 333 157 176 .811 323 166 1.233 .792 -.302 -.336
11 3223 10422 156 175 3067 10247 3448 10662 275 254 3292 10487 0 0 903 2315 619 452 96 100 95 100 13314 13779 .299 3.341 3.186 3.507 3.243 1.438 80 450 3.341 .89 110 3030 8990 37 48 181 192 0 10021 168 9853 3.213 10252 10084 .311 3.063 1.684 1.615
12 1712 1842 143 171 1569 1671 1631 1898 328 275 1488 1727 0 0 573 631 832 577 90 96 40 80 3240 3215 .939 1.065 1.161 1.025 1.051 1.624 52 297 .957 .86 90 3180 8990 38 47 197 206 0 1771 164 1607 1.024 1825 1661 .977 1.116 .034 .158
13 756 745 93 81 663 664 713 726 126 118 620 645 0 0 675 595 134 85 75 71 71 65 1327 1265 .998 1.002 1.04 .945 1.113 2.892 32 145 .942 .81 60 3310 8970 38 44 212 218 0 716 78 638 .963 698 620 1.038 1 -.054 0
14 290 299 102 90 188 209 289 252 138 115 187 162 0 0 117 169 256 76 23 78 0 51 397 349 .9 1.112 .866 .974 .904 3.146 52 277 .999 .5 80 3460 8980 38 46 226 234 0 288 87 201 1.069 242 156 .936 .833 .096 -.264
15 7238 13724 143 162 7095 13562 7111 13444 147 189 6968 13282 0 0 1415 2484 63 229 100 100 100 100 20657 20250 .523 1.911 1.906 1.918 1.863 1.142 52 324 1.964 .96 90 3610 8980 37 46 240 249 0 13196 156 13040 1.838 12927 12771 .544 1.833 .878 .874
16 1634 1886 143 185 1491 1701 1856 2037 157 217 1713 1852 0 0 602 664 71 209 98 96 98 95 3192 3565 .877 1.141 1.081 1.164 1.205 1.81 80 391 1.142 .94 100 3760 8980 37 47 255 265 0 1813 178 1636 1.097 1959 1781 .912 1.04 .134 .056
17 377 565 144 181 233 384 382 566 159 197 238 385 0 0 78 130 72 88 96 98 90 94 617 623 .607 1.648 1.618 1.672 1.723 1.822 52 278 1.608 .74 90 3900 8990 38 47 269 278 0 543 174 369 1.585 544 370 .631 1.555 .664 .637
18 296 453 136 170 160 283 299 458 141 176 163 288 0 0 85 144 40 58 90 94 84 88 443 451 .565 1.769 1.767 1.726 1.973 2.014 52 256 2.028 .7 80 4040 8980 38 46 284 292 0 436 163 272 1.701 440 277 .588 1.699 .766 .765
19 2615 3569 148 178 2467 3391 2692 3744 152 186 2544 3566 0 0 651 1165 45 57 100 100 100 100 5858 6110 .728 1.375 1.402 1.287 1.368 1.451 80 469 1.451 .96 110 4200 8970 35 46 298 309 0 3432 171 3261 1.322 3600 3429 .757 1.348 .402 .431
20 622 692 145 183 477 509 642 694 151 190 497 511 0 0 189 203 46 55 98 98 94 96 986 1008 .937 1.067 1.028 1.061 1.08 1.646 52 249 1.095 .88 80 4350 8990 39 47 315 323 0 665 176 489 1.026 667 491 .975 .989 .037 -.017

Total number of rows: 43008

Table truncated, full table size 9345 Kbytes.




Supplementary data files not provided
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