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Sample GSM741270 Query DataSets for GSM741270
Status Public on Nov 02, 2012
Title shfc21|SW620
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 SW620 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: SW620
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/2006-07/69151.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 2618 3206 378 680 2240 2526 2687 2952 408 740 2309 2272 0 0 665 1009 180 437 100 100 100 97 4766 4581 .887 1.128 .984 1.17 1.14 .51 69 376 1.25 .98 90 2820 4820 61 70 77 86 0 3130 664 2466 1.101 2882 2218 .908 .961 .139 -.058
2 2955 2655 383 681 2572 1974 3045 2579 417 744 2662 1898 0 0 697 932 183 452 100 96 100 87 4546 4560 1.303 .767 .713 .78 .73 .39 52 347 .94 .98 80 2970 4820 62 70 93 101 0 2592 665 1927 .749 2518 1853 1.335 .696 -.416 -.523
3 4888 5410 390 671 4498 4739 4856 5155 410 755 4466 4484 0 0 962 1516 173 454 100 100 100 100 9237 8950 .949 1.054 1.004 1.07 1.04 .37 44 375 1.11 .99 70 3110 4820 62 69 107 114 0 5282 655 4627 1.029 5033 4378 .972 .98 .041 -.029
4 2152 3354 369 650 1783 2704 2181 3235 390 714 1812 2585 0 0 609 1189 162 460 100 98 100 95 4487 4397 .659 1.517 1.427 1.64 1.39 1.19 44 389 1.58 .98 70 3260 4820 62 69 122 129 0 3275 635 2640 1.481 3158 2524 .675 1.393 .566 .478
5 1625 1942 368 717 1257 1225 1601 1881 396 769 1233 1164 0 0 417 757 174 477 100 87 98 56 2482 2397 1.026 .975 .944 1.31 1 1.87 52 362 1.21 .95 80 3410 4820 62 70 137 145 0 1896 700 1196 .951 1836 1136 1.051 .922 -.072 -.118
6 4396 5487 368 665 4028 4822 4435 5202 394 753 4067 4537 0 0 910 1666 188 486 100 100 100 100 8850 8604 .835 1.197 1.116 1.24 1.15 .5 44 390 1.26 .97 70 3550 4820 62 69 151 158 0 5357 649 4708 1.169 5079 4429 .856 1.089 .225 .123
7 1532 1974 395 625 1137 1349 1494 1860 401 695 1099 1235 0 0 537 1095 174 457 98 84 93 64 2486 2334 .843 1.186 1.124 1.57 1.33 1.25 44 379 1.33 .94 70 3700 4820 62 69 166 173 0 1927 610 1317 1.158 1816 1206 .863 1.097 .212 .134
8 3496 4741 370 659 3126 4082 3549 4643 390 705 3179 3984 0 0 1002 1456 169 437 100 98 100 98 7208 7163 .766 1.306 1.253 1.37 1.43 .48 60 334 1.36 .99 80 3850 4810 61 69 181 189 0 4629 643 3985 1.275 4533 3890 .784 1.224 .35 .291
9 2324 3076 359 658 1965 2418 2296 3063 408 742 1937 2405 0 0 535 999 311 482 100 99 100 91 4383 4342 .813 1.231 1.242 1.33 1.27 .71 80 285 1.31 .97 100 3990 4820 61 71 194 204 0 3003 642 2361 1.201 2990 2348 .832 1.212 .265 .278
10 3944 5750 367 631 3577 5119 3899 5798 409 709 3532 5167 0 0 808 1757 306 479 100 100 100 99 8696 8699 .699 1.431 1.463 1.45 1.43 .49 80 268 1.49 .99 100 4140 4820 61 71 209 219 0 5614 616 4998 1.397 5661 5045 .716 1.428 .483 .514
11 1920 2073 401 647 1519 1426 1877 2000 415 732 1476 1353 0 0 472 810 168 464 100 90 100 73 2945 2829 1.065 .939 .917 1.07 .97 .72 70 280 1.07 .96 90 4280 4820 61 70 223 232 0 2024 632 1392 .917 1953 1321 1.091 .895 -.126 -.16
12 3112 4376 392 674 2720 3702 3130 4216 416 752 2738 3542 0 0 806 1460 190 461 100 100 100 99 6422 6280 .735 1.361 1.294 1.45 1.33 .69 80 294 1.42 .98 100 4430 4820 61 71 238 248 0 4272 658 3614 1.329 4116 3458 .753 1.263 .41 .337
13 2410 3553 389 661 2021 2892 2462 3468 418 710 2073 2807 0 0 659 1197 198 416 100 100 99 96 4913 4880 .699 1.431 1.354 1.54 1.41 .84 80 282 1.5 .98 100 4580 4820 61 71 253 263 0 3469 645 2823 1.397 3386 2740 .716 1.322 .482 .403
14 2915 3327 396 640 2519 2687 2819 3191 409 714 2423 2551 0 0 602 1194 170 467 100 96 100 95 5206 4974 .937 1.067 1.053 1.11 1.02 .57 80 282 1.15 .98 100 4720 4820 61 71 267 277 0 3248 625 2623 1.041 3115 2491 .96 1.028 .059 .04
15 1752 1934 388 633 1364 1301 1842 1937 411 712 1454 1304 0 0 414 688 173 453 100 90 99 74 2665 2758 1.048 .954 .897 1.08 .96 .81 80 276 1.1 .96 100 4870 4820 61 71 282 292 0 1888 618 1270 .931 1891 1273 1.074 .876 -.103 -.192
16 9759 12133 422 649 9337 11484 10022 11651 453 724 9600 11002 0 0 1770 2622 202 449 100 100 100 100 20821 20602 .813 1.23 1.146 1.24 1.2 .29 70 300 1.25 .99 90 5010 4820 61 70 296 305 0 11845 634 11212 1.201 11375 10741 .833 1.119 .264 .162
17 3049 4454 436 710 2613 3744 2941 4472 466 802 2505 3762 0 0 766 1325 194 492 100 100 100 97 6357 6267 .698 1.433 1.502 1.52 1.54 .65 70 287 1.47 .98 90 5160 4820 61 70 311 320 0 4348 693 3655 1.399 4366 3673 .715 1.466 .484 .552
18 4028 6173 418 697 3610 5476 4067 6176 437 804 3649 5479 0 0 832 1800 187 523 100 99 99 99 9086 9128 .659 1.517 1.502 1.55 1.47 .54 86 285 1.55 .98 100 5310 4810 60 70 326 336 0 6027 680 5346 1.481 6030 5349 .675 1.466 .567 .552
19 9812 12854 405 634 9407 12220 9798 13080 419 736 9393 12446 0 0 1483 2648 181 492 100 100 100 100 21627 21839 .77 1.299 1.325 1.31 1.3 .32 79 300 1.31 .99 100 5450 4810 60 70 340 350 0 12549 619 11930 1.268 12770 12151 .788 1.294 .343 .371
20 3266 3514 383 604 2883 2910 3232 3481 399 670 2849 2877 0 0 706 1222 177 437 100 99 100 97 5793 5726 .991 1.009 1.01 1.03 .99 .45 86 302 1.11 .98 100 5600 4810 60 70 355 365 0 3431 590 2841 .985 3399 2809 1.015 .986 -.021 -.02

Total number of rows: 41472

Table truncated, full table size 9688 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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