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Sample GSM96045 Query DataSets for GSM96045
Status Public on Feb 25, 2006
Title Ovarian Ca OV282
Sample type RNA
 
Channel 1
Source name CRG Reference
Organism Homo sapiens
Characteristics CRG Reference
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Ovarian Ca OV282_NORWAY
Organism Homo sapiens
Characteristics Ovarian Ca OV282_NORWAY
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Solid tumor, Ovarian
Image: http://smd.stanford.edu/MicroArray/gifs/2001-04/15416.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Feb 07, 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 GPL3001
Series (2)
GSE4198 Ovarian cancers
GSE4268 Breast and ovarian carcinoma

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
VALUE same as UNF_VALUE but with flagged values removed
LOG_RAT2N_MEDIAN 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
UNF_VALUE 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

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 VALUE LOG_RAT2N_MEDIAN UNF_VALUE
1 1356 1368 206 173 1150 1195 1563 1373 246 221 1357 1200 0 0 511 652 201 212 98 93 88 86 2345 2557 .962 1.039 .884 .926 1.065 1.801 80 356 1.14 .93 100 1420 8050 56 66 45 55 -100 1709 216 1493 1.298 1715 1499 .77 1.105 .144 .376
2 878 1532 213 186 665 1346 310 315 446 642 97 129 0 0 971 2067 774 1735 31 31 17 13 2011 226 .494 2.024 1.33 1.471 1.844 3.37 80 254 2.472 .9 100 1550 8050 56 66 58 68 -100 1914 232 1682 2.529 394 161 .395 1.661 .732 1.338
3 5920 3408 218 197 5702 3211 7388 4175 787 821 7170 3978 0 0 4848 2976 1939 1956 63 55 55 51 8913 11148 1.776 .563 .555 .583 .574 3.41 80 247 .576 .88 100 1690 8050 56 66 72 82 -100 4258 246 4011 .704 5216 4970 1.421 .693 -.529 -.507
4 1204 782 210 187 994 595 242 212 752 500 32 25 0 0 2049 1318 1978 1103 16 18 13 13 1589 57 1.671 .599 .781 1.09 .8 3.376 80 247 .585 .94 100 1820 8050 56 66 85 95 -100 977 234 743 .748 265 31 1.337 .976 -.035 -.419
5 2050 2404 214 181 1836 2223 2787 3295 529 515 2573 3114 0 0 1496 1914 1029 1064 60 58 57 56 4059 5687 .826 1.211 1.21 1.256 1.244 2.115 80 247 1.283 .91 100 1960 8050 56 66 99 109 -100 3003 226 2777 1.513 4116 3890 .661 1.512 .596 .597
6 494 492 223 177 271 315 231 166 453 440 8 -11 0 0 906 1142 762 906 8 8 6 6 586 -3 .86 1.162 null 1.722 1.352 3.466 80 247 1.109 .92 100 2090 8050 56 66 112 122 -100 615 221 394 1.452 207 -14 .689 null null .538
7 2365 2403 221 193 2144 2210 3111 3042 485 440 2890 2849 0 0 1817 2047 897 866 58 55 56 55 4354 5739 .97 1.031 .986 .914 1.049 2.537 80 247 1.061 .95 100 2230 8050 56 66 126 136 -100 3002 241 2761 1.288 3800 3559 .777 1.232 .3 .365
8 1643 2503 218 194 1425 2309 1875 2194 632 668 1657 2000 0 0 1291 2193 1044 1240 53 53 45 48 3734 3657 .617 1.62 1.207 1.599 1.65 1.809 80 247 1.521 .91 100 2360 8050 56 66 139 149 -100 3127 242 2885 2.024 2741 2499 .494 1.508 .593 1.017
9 1060 678 220 190 840 488 661 308 420 457 441 118 0 0 999 779 694 982 45 18 26 6 1328 559 1.721 .581 .268 .553 .529 3.253 80 279 1.065 .83 100 2500 8050 56 66 153 163 -100 847 237 610 .726 385 147 1.378 .334 -1.581 -.462
10 2683 3780 222 199 2461 3581 2718 3968 228 209 2496 3769 0 0 471 979 49 81 100 100 100 100 6042 6265 .687 1.455 1.51 1.39 1.474 1.389 80 286 1.559 .95 100 2660 8050 56 66 169 179 0 4722 249 4474 1.818 4957 4709 .55 1.886 .862 .916 .862
11 3979 6559 241 200 3738 6359 4702 7794 243 214 4461 7594 0 0 1862 3532 53 91 96 95 92 91 10097 12055 .588 1.701 1.702 1.531 1.762 2.232 80 220 1.813 .96 100 2800 8060 57 67 183 193 0 8194 250 7944 2.125 9737 9487 .471 2.127 1.088 1.089 1.088
12 3222 5242 254 215 2968 5027 3618 6125 253 235 3364 5910 0 0 1143 2513 56 91 100 95 98 92 7995 9274 .59 1.694 1.757 1.281 1.712 2.263 80 260 1.884 .95 100 2930 8040 55 65 196 206 0 6549 269 6280 2.116 7652 7383 .473 2.195 1.081 1.134 1.081
13 2952 5388 256 239 2696 5149 3079 5549 258 248 2823 5310 0 0 566 1026 57 91 100 100 100 100 7845 8133 .524 1.91 1.881 1.914 1.914 1.149 52 185 1.926 .96 90 3060 8060 57 66 209 218 0 6731 299 6433 2.386 6932 6634 .419 2.35 1.255 1.233 1.255
14 2647 6473 253 233 2394 6240 2779 6895 268 306 2526 6662 0 0 680 2331 113 394 100 97 100 96 8634 9188 .384 2.607 2.637 2.331 2.568 1.855 80 282 2.903 .93 100 3200 8050 56 66 223 233 0 8087 291 7796 3.256 8614 8323 .307 3.295 1.703 1.72 1.703
15 2607 8580 263 295 2344 8285 2920 8627 281 368 2657 8332 0 0 897 3221 121 342 100 100 100 100 10629 10989 .283 3.535 3.136 3.554 3.673 1.604 52 216 3.771 .91 90 3340 8050 56 65 237 246 0 10719 369 10350 4.416 10778 10409 .226 3.918 2.143 1.97 2.143
16 3548 5289 272 291 3276 4998 3869 5217 275 337 3597 4926 0 0 908 1865 56 183 100 100 100 98 8274 8523 .655 1.526 1.369 1.468 1.48 1.719 80 313 1.669 .89 110 3470 8040 54 65 249 260 0 6608 364 6244 1.906 6518 6154 .525 1.711 .931 .775 .931
17 2983 3991 286 277 2697 3714 3468 4354 294 327 3182 4077 0 0 1218 1974 61 174 95 91 93 90 6411 7259 .726 1.377 1.281 1.363 1.314 1.898 80 268 1.551 .89 100 3600 8040 55 65 263 273 0 4986 346 4640 1.72 5439 5093 .581 1.601 .783 .679 .783
18 2324 2603 282 272 2042 2331 2469 2928 294 314 2187 2656 0 0 799 1164 81 173 97 91 95 88 4373 4843 .876 1.142 1.214 1.044 1.134 1.964 80 257 1.294 .89 100 3740 8040 55 65 277 287 0 3252 340 2912 1.426 3658 3318 .701 1.517 .512 .601 .512
19 2223 5263 281 279 1942 4984 2433 5683 290 303 2152 5404 0 0 644 1812 76 154 100 97 98 97 6926 7556 .39 2.566 2.511 2.406 2.562 1.653 80 241 2.754 .94 100 3870 8040 55 65 290 300 0 6575 349 6226 3.206 7100 6751 .312 3.137 1.681 1.649 1.681
20 3023 4864 275 265 2748 4599 3404 5651 275 276 3129 5386 0 0 1027 1925 57 119 100 100 100 96 7347 8515 .598 1.674 1.721 1.575 1.71 1.622 80 264 1.751 .95 110 3990 8050 55 66 301 312 0 6077 331 5746 2.091 7060 6729 .478 2.15 1.064 1.105 1.064

Total number of rows: 44160

Table truncated, full table size 10139 Kbytes.




Supplementary data files not provided
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