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Sample GSM741267 Query DataSets for GSM741267
Status Public on Nov 02, 2012
Title shfc79|SW1116
Sample type genomic
 
Channel 1
Source name Normal human genomic DNA
Organism Homo sapiens
Characteristics reference: Normal human genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SW1116 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: SW1116
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol model: GenePix 4000B
Description Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69147.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 Jun 14, 2011
Last update date Nov 02, 2012
Contact name Keyan Salari
E-mail(s) [email protected]
Organization name Massachusetts General Hospital
Street address Gray/Bigelow Rm 1102, 55 Fruit Street
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
 
Platform ID GPL9073
Series (2)
GSE29953 Colorectal Cancer Cell Lines aCGH
GSE30475 Colorectal Cancer Cells

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 2220 2577 275 533 1945 2044 2155 2514 296 601 1880 1981 0 0 584 889 151 391 100 99 100 91 3989 3861 .952 1.051 1.054 1.13 1.04 .61 69 351 1.2 .97 90 2740 5900 89 98 69 78 0 2193 454 1740 .894 2140 1686 1.118 .897 -.161 -.157
2 2414 2398 266 561 2148 1837 2429 2445 293 630 2163 1884 0 0 576 923 148 398 100 97 100 87 3985 4047 1.169 .855 .871 .88 .85 .48 60 319 1.02 .98 80 2880 5900 90 98 84 92 0 2041 477 1563 .728 2081 1603 1.374 .741 -.458 -.432
3 3889 3885 271 589 3618 3296 3702 4023 297 629 3431 3434 0 0 899 1151 145 391 100 100 100 100 6914 6865 1.098 .911 1.001 .96 .9 .44 52 342 1.02 .98 80 3030 5900 90 98 99 107 0 3307 501 2805 .775 3424 2923 1.29 .852 -.367 -.231
4 1717 2381 271 540 1446 1841 1739 2201 305 591 1468 1661 0 0 528 862 279 383 100 96 98 90 3287 3129 .785 1.273 1.131 1.35 1.3 .62 52 351 1.4 .98 80 3180 5900 90 98 114 122 0 2026 460 1567 1.084 1873 1414 .923 .963 .116 -.054
5 1331 1368 275 486 1056 882 1272 1361 304 560 997 875 0 0 391 481 284 414 100 85 95 57 1938 1872 1.197 .835 .878 .96 .85 .7 60 336 1.06 .95 80 3320 5900 90 98 128 136 0 1164 414 751 .711 1158 745 1.407 .747 -.492 -.421
6 4002 3379 280 525 3722 2854 4012 3297 296 610 3732 2772 0 0 917 1273 143 418 100 98 100 96 6576 6504 1.304 .767 .743 .75 .75 .29 52 342 .87 .98 80 3470 5900 90 98 143 151 0 2876 447 2429 .653 2806 2359 1.532 .632 -.616 -.662
7 1208 1561 272 551 936 1010 1169 1402 288 612 897 851 0 0 376 621 133 405 100 82 100 52 1946 1748 .927 1.079 .949 1.23 .92 .85 44 340 1.33 .97 70 3610 5900 90 97 157 164 0 1329 469 860 .918 1193 724 1.089 .807 -.123 -.309
8 2875 2298 270 542 2605 1756 2874 2230 294 604 2604 1688 0 0 734 935 164 393 100 96 99 87 4361 4292 1.483 .674 .648 .72 .64 .44 70 298 .82 .97 90 3760 5890 88 97 171 180 0 1956 461 1495 .574 1898 1437 1.743 .552 -.802 -.858
9 1820 2332 274 586 1546 1746 1861 2270 298 622 1587 1684 0 0 457 980 140 388 99 94 98 80 3292 3271 .885 1.129 1.061 1.14 1.08 .65 104 253 1.3 .97 110 3900 5890 87 98 184 195 0 1985 499 1486 .961 1932 1433 1.04 .903 -.057 -.147
10 3940 5819 276 547 3664 5272 3953 5670 301 626 3677 5123 0 0 614 1323 157 420 100 100 100 100 8936 8800 .695 1.439 1.393 1.46 1.43 .42 80 235 1.48 .99 100 4050 5900 89 99 200 210 0 4953 466 4487 1.225 4826 4360 .817 1.186 .292 .246
11 1617 1584 279 536 1338 1048 1651 1547 294 592 1372 1011 0 0 340 740 155 398 100 79 100 59 2386 2383 1.277 .783 .737 .88 .86 .55 86 239 .99 .95 100 4190 5900 89 99 214 224 0 1348 456 892 .667 1317 860 1.5 .627 -.585 -.673
12 1489 1980 258 419 1231 1561 1255 1864 285 499 997 1445 0 0 844 1198 141 392 91 80 84 73 2792 2442 .789 1.268 1.449 1.56 1.25 1.14 64 298 1.35 .98 90 4320 5900 89 98 227 236 0 1685 357 1329 1.079 1586 1230 .927 1.234 .11 .303
13 293 360 256 362 37 -2 254 297 281 424 -2 -65 0 0 181 289 144 370 20 14 7 0 35 -67 null null null 5.13 1.41 6.71 69 389 1.21 .47 90 4480 5900 89 98 243 252 -50 306 308 -2 null 253 -55 null null null null
14 3177 3105 263 550 2914 2555 3193 3000 301 597 2930 2450 0 0 911 1177 179 424 99 97 98 93 5469 5380 1.141 .877 .836 .89 .85 .37 86 300 1 .98 100 4640 5890 88 98 259 269 0 2643 468 2175 .746 2553 2085 1.34 .712 -.422 -.491
15 1563 1735 319 685 1244 1050 1499 1684 351 720 1180 999 0 0 390 799 196 452 100 75 100 55 2294 2179 1.185 .844 .847 .97 .76 .84 80 262 1.12 .92 100 4780 5900 89 99 273 283 0 1477 583 894 .718 1433 850 1.392 .721 -.477 -.473
16 11646 13895 329 676 11317 13219 12147 13929 357 753 11818 13253 0 0 2164 2916 183 486 100 100 100 100 24536 25071 .856 1.168 1.121 1.17 1.18 .23 70 293 1.21 .99 90 4930 5890 88 97 288 297 0 11826 575 11251 .994 11855 11280 1.006 .954 -.008 -.067
17 2893 3983 326 611 2567 3372 2887 3892 349 740 2561 3281 0 0 675 1190 175 537 100 100 100 99 5939 5842 .761 1.314 1.281 1.39 1.28 .59 80 240 1.38 .98 100 5070 5900 89 99 302 312 0 3390 520 2870 1.118 3312 2792 .894 1.09 .161 .125
18 4056 4135 328 567 3728 3568 4083 4239 343 634 3755 3672 0 0 740 1375 154 438 100 98 100 97 7296 7427 1.045 .957 .978 .98 .96 .4 97 264 1.05 .99 110 5210 5890 87 98 315 326 0 3519 483 3037 .815 3608 3125 1.228 .832 -.296 -.265
19 10254 10629 294 615 9960 10014 10131 10616 305 658 9837 10001 0 0 2258 2781 147 436 100 100 100 100 19974 19838 .995 1.005 1.017 1.02 1.01 .3 97 267 1.07 .99 110 5360 5890 87 98 330 341 0 9046 523 8523 .856 9035 8512 1.169 .865 -.225 -.209
20 2987 2559 283 614 2704 1945 2948 2432 308 655 2665 1818 0 0 524 891 155 383 100 99 100 93 4649 4483 1.39 .719 .682 .73 .69 .35 86 256 .87 .98 100 5510 5890 88 98 346 356 0 2178 523 1655 .612 2070 1547 1.633 .581 -.708 -.784

Total number of rows: 41472

Table truncated, full table size 9764 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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