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Sample GSM95465 Query DataSets for GSM95465
Status Public on Feb 25, 2006
Title OV433 E2
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 OV433 E2
Organism Homo sapiens
Characteristics CRH vs OV433 E2
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Drug_treatment, Taxol
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/29055.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
1 638 466 132 111 506 355 658 492 144 117 526 381 0 0 262 203 59 46 96 92 94 84 861 907 1.425 .702 .724 .679 .672 1.803 52 293 .718 .88 80 1760 8600 36 44 28 36 0 444 106 338 .668 469 363 1.497 .69 -.582 -.536
2 657 686 142 112 515 574 670 706 151 131 528 594 0 0 272 292 63 92 90 90 84 84 1089 1122 .897 1.115 1.125 1.112 1.063 1.712 32 213 1.127 .87 70 1900 8600 36 43 42 49 0 653 107 547 1.061 672 566 .942 1.071 .086 .1
3 3722 1197 136 107 3586 1090 3951 1282 143 115 3815 1175 0 0 1365 554 53 59 100 96 100 93 4676 4990 3.29 .304 .308 .266 .296 2.089 80 439 .3 .89 110 2060 8600 34 45 56 67 0 1140 102 1038 .289 1221 1119 3.454 .293 -1.788 -1.769
4 3082 4191 134 102 2948 4089 3491 4533 137 105 3357 4431 0 0 1845 2209 42 41 96 100 92 98 7037 7788 .721 1.387 1.32 1.739 1.354 2.324 52 230 1.361 .9 80 2190 8610 37 45 71 79 0 3991 97 3894 1.321 4317 4220 .757 1.257 .402 .33
5 946 1012 132 108 814 904 975 959 136 116 843 851 0 0 485 481 46 46 96 98 88 96 1718 1694 .9 1.111 1.009 1.274 1.057 2.576 52 288 1.105 .85 80 2340 8610 37 45 86 94 0 964 103 861 1.058 913 810 .945 .961 .081 -.057
6 271 286 125 113 146 173 270 264 152 129 145 151 0 0 109 89 183 174 40 46 3 6 319 296 .844 1.185 1.041 1.295 1.042 2.306 32 167 1.086 .7 60 2490 8610 38 44 102 108 0 272 108 165 1.129 251 144 .886 .992 .174 -.012
7 1741 273 138 120 1603 153 1966 273 193 152 1828 153 0 0 838 103 352 251 88 19 76 0 1756 1981 10.477 .095 .084 .095 .089 2.043 52 260 .139 .61 80 2630 8600 36 44 115 123 0 260 114 146 .091 260 146 11.001 .08 -3.46 -3.649
8 4071 4758 129 118 3942 4640 3032 3572 137 123 2903 3454 0 0 3781 4238 64 45 93 97 86 95 8582 6357 .85 1.177 1.19 1.422 1.126 2.859 80 326 1.153 .92 100 2780 8620 37 47 129 139 0 4531 112 4419 1.121 3402 3290 .892 1.133 .165 .18
9 181 206 88 85 93 121 78 108 105 104 -10 23 0 0 375 318 68 96 19 21 11 11 214 13 .769 1.301 null 1.041 .865 4.481 52 256 .835 .64 80 2910 8600 36 44 143 151 0 196 81 115 1.239 103 22 .807 null .309 null
10 302 189 95 88 207 101 241 183 107 96 146 95 0 0 181 82 55 46 75 71 53 50 308 241 2.05 .488 .651 .544 .48 2.753 32 145 .398 .65 60 3080 8620 39 45 161 167 0 180 84 96 .465 174 90 2.152 .62 -1.106 -.69
11 3445 9057 101 104 3344 8953 3640 8943 124 121 3539 8839 0 0 1218 2918 134 101 100 100 100 100 12297 12378 .374 2.677 2.498 2.778 2.72 1.328 80 434 2.694 .96 100 3210 8610 36 46 172 182 0 8626 99 8527 2.55 8517 8418 .392 2.379 1.35 1.25
12 2457 2070 130 137 2327 1933 2184 1766 235 226 2054 1629 0 0 1310 1372 315 236 91 91 91 83 4260 3683 1.204 .831 .793 .756 .771 3.464 12 104 .843 .8 50 3380 8600 37 42 191 196 0 1971 130 1841 .791 1682 1551 1.264 .755 -.338 -.405
13 988 1317 102 112 886 1205 1034 1375 123 125 932 1263 0 0 529 667 100 99 92 96 88 90 2091 2195 .735 1.36 1.355 1.371 1.387 2.11 52 228 1.395 .9 80 3510 8620 38 46 203 211 0 1254 107 1148 1.295 1310 1203 .772 1.291 .373 .368
14 73 98 74 90 -1 8 72 93 86 98 -2 3 0 0 22 42 42 45 3 17 0 5 7 1 null null null 2.249 1.813 4.158 52 246 2.106 .15 80 3640 8600 36 44 216 224 0 93 86 8 null 89 3 null null null null
15 141 185 62 78 79 107 119 137 67 86 57 59 0 0 73 211 23 42 86 59 59 28 186 116 .738 1.354 1.035 .964 1.222 3.655 52 256 4.543 .39 80 3790 8600 36 44 231 239 0 176 74 102 1.29 130 56 .775 .986 .367 -.021
16 83 96 66 90 17 6 80 99 73 95 14 9 0 0 32 40 26 44 34 17 11 1 23 23 2.833 .353 .643 1.342 1.353 3.428 52 256 6.376 .15 80 3930 8600 36 44 245 253 0 91 86 6 .336 94 9 2.975 .612 -1.573 -.708
17 83 112 67 95 16 17 65 111 73 100 -2 16 0 0 58 45 27 38 25 28 13 11 33 14 .941 1.063 null 1.312 1.679 4.088 52 256 1.602 .09 80 4080 8600 36 44 260 268 0 107 90 16 1.012 106 15 .988 null .017 null
18 74 88 67 88 7 0 66 88 74 94 -1 0 0 0 28 32 27 36 15 7 7 1 7 -1 null null null 1.709 1.556 4.543 52 256 10.165 .07 80 4220 8600 36 44 274 282 0 84 84 0 null 84 0 null null null null
19 82 111 71 92 11 19 76 107 78 98 5 15 0 0 29 43 28 45 26 28 7 1 30 20 .579 1.727 3 .989 1.305 3.721 52 266 .53 .68 80 4370 8600 36 44 289 297 0 106 88 18 1.645 102 14 .608 2.857 .718 1.515
20 74 114 73 94 1 20 66 102 78 100 -7 8 0 0 27 43 29 40 19 32 3 9 21 1 .05 20 null 1.345 1.211 4.305 52 256 22.553 .03 80 4520 8600 36 44 304 312 0 109 90 19 19.048 97 8 .053 null 4.252 null

Total number of rows: 43008

Table truncated, full table size 9256 Kbytes.




Supplementary data files not provided
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