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Sample GSM95470 Query DataSets for GSM95470
Status Public on Feb 25, 2006
Title MESOV T40
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 MESOV T40
Organism Homo sapiens
Characteristics CRH vs MESOV T40
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Drug_treatment, Taxol
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/29347.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
1 522 246 153 89 369 157 509 241 160 92 356 152 0 0 151 75 49 33 96 96 96 84 526 508 2.35 .425 .427 .424 .404 1.936 32 226 .389 .73 70 1530 8950 43 50 33 40 0 234 85 150 .405 230 145 2.468 .407 -1.303 -1.298
2 599 393 155 88 444 305 592 353 167 103 437 265 0 0 179 155 64 54 100 100 100 91 749 702 1.456 .687 .606 .661 .622 1.442 12 104 .723 .86 50 1670 8950 44 49 48 53 0 374 84 290 .654 336 252 1.529 .578 -.612 -.792
3 2987 350 154 92 2833 258 3327 350 159 97 3173 258 0 0 1278 175 45 38 98 88 98 82 3091 3431 10.981 .091 .081 .089 .089 1.928 80 427 .089 .84 100 1840 8950 42 52 63 73 0 333 88 246 .087 333 246 11.53 .077 -3.527 -3.691
4 1720 3017 150 95 1570 2922 1704 2750 152 103 1554 2655 0 0 993 2118 40 39 100 100 98 100 4492 4209 .537 1.861 1.708 1.653 1.906 2.278 52 248 2.105 .88 80 1990 8960 44 52 79 87 0 2873 90 2783 1.773 2619 2529 .564 1.627 .826 .702
5 774 324 157 102 617 222 760 347 167 112 603 245 0 0 188 117 73 65 100 87 100 75 839 848 2.779 .36 .406 .336 .396 1.86 32 216 .342 .79 70 2120 8950 43 50 92 99 0 309 97 211 .343 330 233 2.918 .387 -1.545 -1.37
6 301 200 167 93 134 107 261 196 163 95 94 103 0 0 100 63 46 36 91 91 50 58 241 197 1.252 .799 1.096 .816 .89 3.501 12 104 .444 .46 50 2280 8950 44 49 109 114 0 190 89 102 .76 187 98 1.315 1.044 -.395 .062
7 1360 250 159 99 1201 151 1422 247 174 107 1263 148 0 0 293 68 124 40 100 93 96 84 1352 1411 7.954 .126 .117 .116 .125 1.614 32 221 .101 .73 70 2410 8950 43 50 121 128 0 238 94 144 .12 235 141 8.351 .112 -3.062 -3.164
8 2638 3406 155 99 2483 3307 2171 3011 167 105 2016 2912 0 0 1974 2502 96 50 95 100 92 100 5790 4928 .751 1.332 1.444 1.485 1.283 2.583 80 399 1.327 .91 100 2570 8960 43 53 136 146 0 3244 94 3150 1.268 2868 2773 .788 1.376 .343 .46
9 802 1124 155 98 647 1026 924 1158 163 108 769 1060 0 0 365 383 44 45 93 100 90 100 1673 1829 .631 1.586 1.378 1.886 1.691 1.737 32 189 1.436 .92 70 2700 8960 44 51 150 157 0 1070 93 977 1.51 1103 1010 .662 1.313 .595 .393
10 280 432 118 81 162 351 137 112 124 88 19 31 0 0 381 751 63 44 44 48 28 34 513 50 .462 2.167 1.632 1.03 .945 3.084 52 298 2.429 .71 80 2850 8950 43 51 165 173 0 411 77 334 2.063 107 30 .485 1.554 1.045 .636
11 635 555 62 45 573 510 215 108 72 47 153 63 0 0 989 922 35 17 84 75 75 65 1083 216 1.124 .89 .412 .45 .461 3.645 32 114 .912 .82 60 3010 8900 39 45 182 188 0 529 43 486 .848 103 60 1.18 .392 -.238 -1.35
12 1489 1558 123 80 1366 1478 1355 1297 130 87 1232 1217 0 0 1069 1093 68 46 87 96 87 90 2844 2449 .924 1.082 .988 1.126 1.111 1.798 32 214 1.052 .93 70 3160 8960 44 51 196 203 0 1484 76 1408 1.03 1235 1159 .97 .941 .043 -.088
13 678 687 156 99 522 588 665 616 166 119 509 517 0 0 304 361 67 114 94 88 86 84 1110 1026 .888 1.126 1.016 1.113 1.142 2.104 52 264 1.149 .87 80 3290 8960 44 52 209 217 0 654 94 560 1.073 587 492 .932 .967 .101 -.048
14 338 198 164 89 174 109 338 189 271 109 174 100 0 0 64 62 675 107 0 33 0 8 283 274 1.596 .626 .575 .576 .537 2.032 12 104 .568 .55 50 3440 8950 44 49 225 230 0 189 85 104 .597 180 95 1.676 .547 -.745 -.869
15 4474 5014 157 106 4317 4908 4321 4841 205 124 4164 4735 0 0 3194 3458 525 247 85 96 72 90 9225 8899 .88 1.137 1.137 1.219 1.136 2.266 80 458 1.131 .9 110 3580 8960 42 53 236 247 0 4775 101 4674 1.083 4610 4510 .924 1.083 .115 .115
16 1581 1459 152 104 1429 1355 1518 1539 160 109 1366 1435 0 0 996 806 73 39 98 96 86 94 2784 2801 1.055 .948 1.051 1.012 .841 2.583 52 273 .87 .88 80 3730 8970 45 53 253 261 0 1390 99 1290 .903 1466 1367 1.107 1 -.147 .001
17 382 290 158 93 224 197 391 307 164 107 233 214 0 0 121 98 56 48 90 90 78 75 421 447 1.137 .879 .918 .865 .873 2.103 32 166 .76 .69 60 3870 8950 44 50 268 274 0 276 89 188 .838 292 204 1.194 .875 -.256 -.193
18 322 235 158 104 164 131 309 219 161 118 151 115 0 0 108 84 43 64 87 81 84 40 295 266 1.252 .799 .762 .696 .775 2.471 32 158 .813 .57 60 4030 8950 44 50 284 290 0 224 99 125 .761 209 110 1.315 .725 -.395 -.463
19 2311 2873 165 111 2146 2762 2507 3076 172 119 2342 2965 0 0 957 1117 63 52 97 100 97 100 4908 5307 .777 1.287 1.266 1.326 1.224 1.989 80 416 1.274 .93 110 4170 8960 42 53 295 306 0 2736 106 2630 1.226 2930 2824 .816 1.206 .294 .27
20 647 412 173 106 474 306 632 465 195 115 459 359 0 0 199 155 97 58 96 93 90 87 780 818 1.549 .646 .782 .551 .637 1.824 32 152 .606 .82 60 4310 8950 44 50 312 318 0 392 101 291 .615 443 342 1.626 .745 -.702 -.425

Total number of rows: 43008

Table truncated, full table size 9313 Kbytes.




Supplementary data files not provided
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