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Sample GSM741254 Query DataSets for GSM741254
Status Public on Nov 02, 2012
Title shfc80|RKO
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 RKO genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: RKO
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/2006-07/69146.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 1401 1524 340 561 1061 963 1387 1458 357 641 1047 897 0 0 350 678 154 417 100 75 100 54 2024 1944 1.102 .908 .857 1.1 .83 .97 69 346 1.1 .92 90 2740 6090 84 93 65 74 0 1619 596 1023 .964 1549 953 1.037 .91 -.052 -.135
2 1444 1088 361 602 1083 486 1417 898 376 658 1056 296 0 0 322 577 150 419 100 43 100 20 1569 1352 2.228 .449 .28 .55 .48 .55 60 303 .8 .87 80 2880 6090 85 93 80 88 0 1156 640 516 .477 954 315 2.097 .298 -1.068 -1.747
3 2324 1963 360 556 1964 1407 2248 1882 372 627 1888 1326 0 0 515 825 143 417 100 94 100 77 3371 3214 1.396 .716 .702 .78 .66 .54 52 339 .85 .96 80 3030 6090 85 93 95 103 0 2086 591 1495 .761 2000 1409 1.314 .746 -.394 -.422
4 1098 1593 348 565 750 1028 1097 1536 362 624 749 971 0 0 322 659 141 404 98 79 94 60 1778 1720 .73 1.371 1.296 1.7 1.39 1.22 52 323 1.46 .94 80 3180 6090 85 93 110 118 0 1693 600 1092 1.456 1632 1032 .687 1.378 .542 .462
5 757 1174 348 565 409 609 738 1107 369 651 390 542 0 0 321 652 153 424 72 56 59 31 1018 932 .672 1.489 1.39 3.37 1.82 4.35 64 311 1.55 .91 90 3310 6090 84 93 122 131 0 1248 600 647 1.582 1176 576 .632 1.477 .662 .562
6 2292 2346 361 574 1931 1772 2331 2326 382 667 1970 1752 0 0 483 974 165 437 100 92 100 77 3703 3722 1.09 .918 .889 .94 .94 .54 52 345 1.03 .97 80 3470 6090 85 93 139 147 0 2493 610 1883 .975 2472 1862 1.026 .945 -.036 -.082
7 653 1216 355 625 298 591 589 1099 370 682 234 474 0 0 344 695 159 421 58 53 42 30 889 708 .504 1.983 2.026 2.66 2.13 2.43 64 278 1.85 .91 90 3620 6100 85 94 153 162 0 1292 664 628 2.107 1168 504 .475 2.152 1.075 1.106
8 1481 1221 385 670 1096 551 1449 1156 393 709 1064 486 0 0 346 606 154 409 100 53 99 26 1647 1550 1.989 .503 .457 .75 .56 .72 70 284 .87 .89 90 3760 6080 83 92 167 176 0 1297 712 586 .534 1228 516 1.872 .485 -.905 -1.043
9 1210 1223 382 683 828 540 1191 1143 394 729 809 460 0 0 315 587 162 413 99 55 97 31 1368 1269 1.533 .652 .569 .97 .83 1.12 86 269 1.03 .89 100 3900 6080 83 93 181 191 0 1300 726 574 .693 1215 489 1.443 .604 -.529 -.727
10 2097 2229 375 631 1722 1598 2064 2078 388 709 1689 1447 0 0 428 791 162 424 100 98 100 82 3320 3136 1.078 .928 .857 .98 .84 .57 80 253 1.05 .97 100 4050 6090 84 94 196 206 0 2369 671 1698 .986 2208 1538 1.014 .91 -.02 -.135
11 985 1135 360 654 625 481 924 1070 377 739 564 416 0 0 297 513 150 458 96 48 89 19 1106 980 1.299 .77 .738 1.37 .85 1.45 84 256 1.18 .87 100 4190 6090 84 94 210 220 0 1206 695 511 .818 1137 442 1.223 .784 -.29 -.351
12 1310 1476 378 636 932 840 1323 1447 391 721 945 811 0 0 357 711 153 430 99 70 98 46 1772 1756 1.11 .901 .858 1.24 1 .98 80 265 1.11 .92 100 4340 6090 84 94 225 235 0 1568 676 893 .958 1538 862 1.044 .912 -.062 -.133
13 1520 1910 368 609 1152 1301 1530 1884 381 678 1162 1275 0 0 364 723 152 406 100 89 100 70 2453 2437 .885 1.129 1.097 1.23 1.16 .76 80 260 1.26 .96 100 4490 6090 84 94 240 250 0 2030 647 1382 1.2 2002 1355 .833 1.166 .263 .222
14 1685 1866 342 648 1343 1218 1606 1829 365 701 1264 1181 0 0 426 754 149 417 100 86 99 66 2561 2445 1.103 .907 .934 1.04 .91 .71 97 270 1.14 .95 110 4630 6080 82 93 253 264 0 1983 689 1294 .964 1944 1255 1.038 .993 -.053 -.01
15 846 1110 343 656 503 454 850 1038 367 687 507 382 0 0 240 534 168 379 93 50 77 21 957 889 1.108 .903 .753 1.21 .83 1.31 80 257 1.32 .91 100 4780 6090 84 94 269 279 0 1180 697 482 .959 1103 406 1.043 .801 -.06 -.321
16 4822 5451 354 678 4468 4773 4844 5347 373 731 4490 4669 0 0 863 1294 170 418 100 100 100 100 9241 9159 .936 1.068 1.04 1.08 1.05 .32 80 277 1.15 .99 100 4930 6090 84 94 284 294 0 5792 720 5072 1.135 5682 4961 .881 1.105 .183 .144
17 1586 2325 372 693 1214 1632 1665 2205 374 756 1293 1512 0 0 392 848 143 450 100 94 99 85 2846 2805 .744 1.344 1.169 1.53 1.45 1 86 243 1.48 .98 100 5070 6090 84 94 298 308 0 2471 736 1734 1.428 2343 1607 .7 1.243 .514 .313
18 1760 2079 372 668 1388 1411 1775 2007 384 739 1403 1339 0 0 388 805 155 436 100 90 98 77 2799 2742 .984 1.017 .954 1.12 1.06 .65 97 254 1.19 .96 110 5210 6080 82 93 311 322 0 2209 710 1499 1.08 2133 1423 .926 1.014 .111 .02
19 3859 4616 374 706 3485 3910 3658 4703 385 784 3284 3997 0 0 983 1210 162 472 100 99 100 98 7395 7281 .891 1.122 1.217 1.19 1.18 .49 97 272 1.23 .97 110 5360 6080 82 93 326 337 0 4905 750 4155 1.192 4997 4247 .839 1.293 .254 .371
20 1038 1421 349 730 689 691 1022 1296 372 802 673 566 0 0 276 638 150 484 97 60 94 26 1380 1239 .997 1.003 .841 1.4 1.15 1.36 97 278 1.39 .91 110 5510 6080 82 93 341 352 0 1510 776 734 1.066 1377 601 .938 .894 .092 -.162

Total number of rows: 41472

Table truncated, full table size 9525 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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