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Sample GSM741247 Query DataSets for GSM741247
Status Public on Nov 02, 2012
Title shfc110|DLD1
Sample type genomic
 
Channel 1
Source name Normal human male genomic DNA
Organism Homo sapiens
Characteristics reference: Normal human male genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name DLD1 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: DLD1
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/2006-06/68859.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 2042 1469 328 584 1714 885 2052 1420 343 640 1724 836 0 0 420 656 135 432 100 70 100 47 2599 2560 1.937 .516 .485 .58 .54 .4 80 308 .74 .92 100 2550 5330 60 70 82 92 0 1457 579 878 .512 1408 829 1.953 .481 -.966 -1.056
2 1851 2145 333 595 1518 1550 1816 1948 349 642 1483 1353 0 0 458 863 135 413 100 91 100 83 3068 2836 .979 1.021 .912 1.07 .97 .6 69 313 1.17 .97 90 2690 5320 59 68 96 105 0 2127 590 1537 1.013 1932 1342 .988 .905 .018 -.144
3 3121 3156 353 625 2768 2531 3265 3016 767 716 2912 2391 0 0 706 1193 4263 532 0 94 0 91 5299 5303 1.094 .914 .821 .91 .9 .39 70 320 1.03 .98 90 2840 5320 59 68 111 120 0 3130 620 2510 .907 2991 2371 1.103 .814 -.141 -.297
4 1612 2264 357 572 1255 1692 1616 2241 366 648 1259 1669 0 0 423 991 138 434 100 90 100 76 2947 2928 .742 1.348 1.326 1.47 1.19 .89 51 345 1.41 .97 80 2980 5320 60 68 126 134 0 2245 567 1678 1.337 2222 1655 .748 1.315 .419 .395
5 1252 1591 347 607 905 984 1206 1467 366 662 859 860 0 0 398 776 150 443 99 76 96 49 1889 1719 .92 1.087 1.001 1.35 1.12 .96 70 332 1.28 .92 90 3130 5320 59 68 140 149 0 1578 602 976 1.078 1455 853 .927 .993 .109 -.01
6 2554 3551 367 548 2187 3003 2593 3449 379 623 2226 2901 0 0 706 1342 149 428 100 100 100 98 5190 5127 .728 1.373 1.303 1.44 1.32 .7 60 351 1.4 .97 80 3280 5320 60 68 156 164 0 3521 543 2978 1.362 3420 2877 .734 1.292 .445 .37
7 986 1363 360 527 626 836 973 1367 370 622 613 840 0 0 294 613 145 444 93 73 89 48 1462 1453 .749 1.335 1.37 2.39 1.59 5.06 44 348 1.35 .95 70 3430 5320 60 67 171 178 0 1352 523 829 1.324 1356 833 .755 1.359 .405 .442
8 2286 2622 365 525 1921 2097 2332 2375 378 637 1967 1850 0 0 584 1171 137 455 100 94 100 86 4018 3817 .916 1.092 .941 1.13 .97 .72 70 274 1.16 .96 90 3570 5320 59 68 184 193 0 2600 521 2079 1.082 2355 1835 .924 .933 .114 -.101
9 1484 1832 375 565 1109 1267 1505 1778 383 649 1130 1213 0 0 434 772 147 380 96 89 95 72 2376 2343 .875 1.142 1.073 1.46 1.06 1.88 115 223 1.23 .96 120 3710 5320 58 70 197 209 0 1817 560 1256 1.133 1763 1203 .883 1.064 .18 .09
10 2751 3680 345 589 2406 3091 2779 3551 367 660 2434 2962 0 0 563 1184 143 405 100 99 100 98 5497 5396 .778 1.285 1.217 1.35 1.25 .62 104 220 1.33 .98 110 3860 5320 58 69 212 223 0 3649 584 3065 1.274 3521 2937 .785 1.207 .349 .271
11 1326 1445 374 577 952 868 1324 1261 386 673 950 684 0 0 324 618 148 463 100 68 100 46 1820 1634 1.097 .912 .72 1.09 .93 .8 97 249 1.1 .94 110 4000 5320 58 69 226 237 0 1433 572 861 .904 1250 678 1.106 .714 -.145 -.486
12 1694 2165 372 583 1322 1582 1665 2057 381 688 1293 1474 0 0 359 869 144 454 100 95 99 80 2904 2767 .836 1.197 1.14 1.32 1.23 .71 97 261 1.29 .97 110 4150 5320 58 69 241 252 0 2147 578 1569 1.187 2040 1462 .843 1.13 .247 .177
13 2067 3467 394 666 1673 2801 2086 3243 402 713 1692 2577 0 0 436 1156 156 423 99 99 99 99 4474 4269 .597 1.674 1.523 1.92 1.69 1.86 86 253 1.68 .98 100 4300 5320 59 69 257 267 0 3438 660 2778 1.66 3216 2555 .602 1.51 .731 .595
14 2484 2714 435 556 2049 2158 2524 2694 451 624 2089 2138 0 0 507 1002 163 397 100 97 100 90 4207 4227 .949 1.053 1.023 1.1 1.01 .58 104 236 1.11 .97 110 4440 5320 58 69 270 281 0 2691 551 2140 1.044 2671 2120 .958 1.015 .063 .021
15 1342 1259 570 584 772 675 1343 1147 563 641 773 563 0 0 343 651 197 416 95 63 92 35 1447 1336 1.144 .874 .728 1.57 .83 3 97 242 .93 .89 110 4590 5320 58 69 285 296 0 1248 579 669 .867 1137 558 1.153 .722 -.206 -.469
16 7320 8029 589 629 6731 7400 7403 8100 576 688 6814 7471 0 0 1236 1380 191 433 100 100 100 100 14131 14285 .91 1.099 1.096 1.17 1.09 .6 86 251 1.09 .99 100 4740 5320 59 69 301 311 0 7962 624 7338 1.09 8032 7408 .917 1.087 .125 .121
17 2455 2633 489 589 1966 2044 2511 2451 494 683 2022 1862 0 0 457 1073 191 498 100 94 100 84 4010 3884 .962 1.04 .921 1.07 1.01 .52 86 245 1.07 .98 100 4880 5320 59 69 315 325 0 2611 584 2027 1.031 2430 1846 .97 .913 .044 -.131
18 2890 3724 375 601 2515 3123 2979 3617 386 669 2604 3016 0 0 593 1119 150 452 100 100 100 100 5638 5620 .805 1.242 1.158 1.29 1.23 .54 104 222 1.29 .98 110 5030 5320 58 69 329 340 0 3693 596 3097 1.231 3587 2991 .812 1.149 .3 .2
19 6144 6542 368 577 5776 5965 6207 6541 376 635 5839 5964 0 0 1316 1820 131 418 100 99 100 99 11741 11803 .968 1.033 1.021 1.04 1.04 .34 104 221 1.08 .99 110 5170 5320 58 69 343 354 0 6487 572 5915 1.024 6486 5914 .976 1.013 .034 .018
20 1864 1781 358 549 1506 1232 1850 1678 370 590 1492 1129 0 0 407 729 124 403 100 88 100 65 2738 2621 1.222 .818 .757 .86 .72 .59 104 231 .98 .97 110 5320 5320 58 69 358 369 0 1766 544 1222 .811 1664 1120 1.233 .75 -.302 -.414

Total number of rows: 41472

Table truncated, full table size 9523 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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