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Sample GSM95468 Query DataSets for GSM95468
Status Public on Feb 25, 2006
Title MESOV TxT50 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 MESOV TxT50 CGH
Organism Homo sapiens
Characteristics MESOV TxT50 CGH
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Drug_treatment, Taxol
Image: http://smd.stanford.edu/MicroArray/gifs/2003-01/37238.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
1 689 483 212 169 477 314 653 488 219 176 441 319 0 0 159 88 65 54 100 100 100 100 791 760 1.519 .658 .723 .661 .664 1.324 12 104 .636 .83 50 2010 7060 43 48 58 63 0 577 202 375 .786 583 381 1.273 .863 -.348 -.212
2 983 776 208 167 775 609 1111 820 255 175 903 653 0 0 517 397 354 63 68 87 59 81 1384 1556 1.273 .786 .723 .806 .802 1.37 32 197 .796 .97 70 2150 7070 43 50 71 78 0 926 199 727 .938 979 779 1.066 .863 -.092 -.212
3 303 220 205 165 98 55 228 198 211 169 23 33 0 0 222 94 47 50 30 42 23 15 153 56 1.782 .561 1.435 .895 .883 4.085 52 268 .464 .73 80 2280 7060 42 50 84 92 0 263 197 66 .67 236 39 1.493 1.713 -.578 .776
4 524 375 200 169 324 206 500 354 207 172 300 185 0 0 276 169 45 41 81 78 65 75 530 485 1.573 .636 .617 .795 .648 2.437 32 170 .601 .89 60 2440 7060 43 49 101 107 0 448 202 246 .759 423 221 1.318 .736 -.398 -.442
5 1150 944 203 164 947 780 1142 1013 207 168 939 849 0 0 501 360 38 45 96 100 96 96 1727 1788 1.214 .824 .904 .852 .855 1.241 32 215 .78 .97 70 2590 7070 43 50 115 122 0 1127 196 931 .983 1209 1013 1.017 1.079 -.024 .11
6 712 488 199 160 513 328 631 459 213 171 432 299 0 0 333 231 63 50 93 87 87 81 841 731 1.564 .639 .692 .607 .602 1.607 32 189 .629 .91 70 2730 7080 44 51 129 136 0 583 191 392 .763 548 357 1.31 .826 -.39 -.275
7 889 652 194 169 695 483 933 633 197 170 739 464 0 0 344 243 36 41 100 96 100 93 1178 1203 1.439 .695 .628 .701 .683 1.334 32 159 .7 .95 60 2890 7070 44 50 146 152 0 778 202 577 .83 756 554 1.205 .749 -.27 -.416
8 949 817 199 169 750 648 967 893 209 173 768 724 0 0 403 333 54 51 96 93 93 93 1398 1492 1.157 .864 .943 .845 .838 1.54 32 145 .846 .96 70 3010 7080 44 51 157 164 0 975 202 773 1.031 1066 864 .97 1.125 .044 .17
9 1037 788 193 167 844 621 1039 803 199 171 846 636 0 0 256 202 47 47 100 100 100 100 1465 1482 1.359 .736 .752 .731 .737 1.235 80 306 .739 .96 100 3140 7070 42 52 169 179 0 941 199 741 .878 959 759 1.139 .897 -.187 -.156
10 401 282 188 164 213 118 390 279 192 164 202 115 0 0 94 76 41 41 97 85 92 65 331 317 1.805 .554 .569 .516 .549 2.186 80 286 .569 .69 100 3290 7070 42 52 184 194 0 337 196 141 .661 333 137 1.512 .68 -.597 -.557
11 902 645 196 162 706 483 945 653 202 164 749 491 0 0 318 224 43 41 98 98 97 95 1189 1240 1.462 .684 .656 .685 .702 1.436 80 296 .692 .95 100 3430 7070 42 52 198 208 0 770 193 577 .817 779 586 1.225 .782 -.292 -.354
12 704 501 193 157 511 344 674 487 197 160 481 330 0 0 259 184 37 39 100 98 100 97 855 811 1.485 .673 .686 .657 .684 1.44 80 305 .682 .94 100 3580 7070 42 52 213 223 0 598 187 411 .804 581 394 1.244 .819 -.316 -.288
13 947 821 190 151 757 670 955 842 192 153 765 691 0 0 282 206 35 41 100 100 100 100 1427 1456 1.13 .885 .903 .912 .895 1.273 80 339 .86 .96 110 3730 7070 41 52 227 238 0 980 180 800 1.056 1005 825 .947 1.078 .079 .109
14 886 544 191 140 695 404 932 570 209 152 741 430 0 0 258 163 100 63 98 97 96 90 1099 1171 1.72 .581 .58 .554 .561 1.414 80 398 .589 .95 110 3870 7060 40 51 241 252 0 649 167 482 .694 680 513 1.441 .693 -.527 -.53
15 762 594 191 147 571 447 776 611 214 161 585 464 0 0 150 103 104 64 100 100 96 100 1018 1049 1.277 .783 .793 .794 .796 1.283 80 397 .74 .93 110 4020 7070 41 52 256 267 0 709 175 534 .934 729 554 1.07 .947 -.098 -.079
16 209 163 185 154 24 9 204 159 195 157 19 5 0 0 51 54 49 42 32 26 7 9 33 24 2.667 .375 .263 .845 1.036 4.151 52 232 .741 .8 80 4180 7060 42 50 274 282 0 195 184 11 .448 190 6 2.234 .314 -1.16 -1.671
17 1347 982 192 152 1155 830 1476 1110 199 153 1284 958 0 0 538 378 57 43 93 95 92 93 1985 2242 1.392 .719 .746 .747 .714 1.3 80 382 .72 .98 110 4310 7060 40 51 285 296 0 1172 181 991 .858 1325 1144 1.166 .891 -.221 -.167
18 216 171 188 157 28 14 195 156 200 161 7 -1 0 0 104 85 57 43 17 19 7 11 42 6 2 .5 null .919 1.034 4.544 52 211 .621 .65 80 4470 7060 42 50 303 311 0 204 187 17 .597 186 -1 1.676 null -.745 null
19 3100 2918 191 163 2909 2755 3325 3250 206 175 3134 3087 0 0 1267 1160 95 87 95 95 93 93 5664 6221 1.056 .947 .985 .986 .958 1.453 80 358 .936 .99 110 4600 7060 40 51 314 325 0 3483 195 3289 1.13 3879 3685 .885 1.176 .177 .234
20 1046 1022 194 159 852 863 1088 1045 208 172 894 886 0 0 338 338 95 93 98 97 92 93 1715 1780 .987 1.013 .991 1.022 .991 1.273 80 310 1.02 .97 100 4750 7060 41 51 330 340 0 1220 190 1030 1.209 1247 1058 .827 1.183 .274 .242

Total number of rows: 43104

Table truncated, full table size 9681 Kbytes.




Supplementary data files not provided
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