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Sample GSM741253 Query DataSets for GSM741253
Status Public on Nov 02, 2012
Title shfc76|NCIH508
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 NCIH508 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: NCIH508
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/2006-07/69150.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 2310 2438 318 606 1992 1832 2322 2530 349 648 2004 1924 0 0 586 858 174 384 100 96 100 87 3824 3928 1.087 .92 .96 .99 .98 .61 70 340 1.07 .98 90 2620 5710 102 111 69 78 0 2469 614 1855 .931 2562 1948 1.074 .972 -.103 -.041
2 2608 2212 305 560 2303 1652 2671 2038 329 642 2366 1478 0 0 752 985 159 376 98 95 98 87 3955 3844 1.394 .717 .625 .86 .63 1.28 60 320 .87 .96 80 2760 5710 103 111 84 92 0 2240 567 1673 .726 2064 1497 1.377 .633 -.461 -.661
3 3439 2991 338 547 3101 2444 3364 2912 356 609 3026 2365 0 0 858 960 169 380 100 100 100 98 5545 5391 1.269 .788 .782 .82 .74 .4 60 348 .88 .99 80 2910 5710 103 111 99 107 0 3029 554 2475 .798 2949 2395 1.253 .792 -.325 -.337
4 1555 1844 329 588 1226 1256 1531 1904 342 648 1202 1316 0 0 373 677 165 398 100 91 98 73 2482 2518 .976 1.024 1.095 1.1 .97 .76 44 370 1.22 .97 70 3050 5710 103 110 113 120 0 1867 595 1272 1.038 1928 1333 .964 1.109 .053 .149
5 973 1101 322 613 651 488 936 1035 340 679 614 422 0 0 341 515 150 394 96 54 84 22 1139 1036 1.334 .75 .687 .93 .72 .77 69 356 1.16 .89 90 3200 5710 102 111 127 136 0 1115 621 494 .759 1048 427 1.317 .696 -.398 -.523
6 3436 3186 320 581 3116 2605 3459 3078 337 650 3139 2497 0 0 704 957 155 401 100 98 100 98 5721 5636 1.196 .836 .795 .85 .86 .33 52 350 .94 .98 80 3350 5710 103 111 143 151 0 3227 588 2638 .847 3117 2529 1.181 .806 -.24 -.312
7 1037 1225 315 530 722 695 984 1131 331 607 669 601 0 0 358 624 154 383 100 66 89 39 1417 1270 1.039 .963 .898 1.47 1.03 1.77 44 348 1.24 .96 70 3490 5710 103 110 157 164 0 1241 537 704 .975 1145 609 1.026 .91 -.037 -.136
8 3145 1812 318 577 2827 1235 2886 1677 331 627 2568 1100 0 0 2213 813 144 379 100 87 100 69 4062 3668 2.289 .437 .428 .54 .45 .42 86 274 .6 .9 100 3640 5710 102 112 171 181 0 1835 584 1251 .442 1698 1114 2.26 .434 -1.177 -1.205
9 1617 1569 314 592 1303 977 1628 1576 329 638 1314 984 0 0 428 629 146 391 99 80 99 60 2280 2298 1.334 .75 .749 .86 .81 .52 97 272 1 .96 110 3780 5700 100 111 184 195 0 1589 600 989 .759 1596 997 1.317 .758 -.397 -.399
10 3458 3691 335 607 3123 3084 3404 3486 357 669 3069 2879 0 0 566 1022 159 402 100 100 100 100 6207 5948 1.013 .988 .938 1 .97 .36 80 248 1.06 .98 100 3930 5710 102 112 200 210 0 3738 615 3123 1 3530 2916 1 .95 0 -.074
11 1328 1429 369 622 959 807 1305 1323 366 672 936 701 0 0 353 642 162 386 100 74 100 43 1766 1637 1.188 .842 .749 .98 .85 .75 86 259 1.08 .95 100 4070 5710 102 112 214 224 0 1447 630 817 .852 1340 710 1.173 .758 -.231 -.399
12 1918 1915 362 593 1556 1322 1895 1871 376 649 1533 1278 0 0 414 746 177 387 100 93 100 75 2878 2811 1.177 .85 .834 .92 .81 .58 80 279 1 .97 100 4220 5710 102 112 229 239 0 1939 601 1339 .86 1895 1294 1.162 .844 -.217 -.244
13 2263 2322 334 610 1929 1712 2242 2281 367 641 1908 1671 0 0 464 722 175 377 100 96 100 93 3641 3579 1.127 .888 .876 .92 .89 .46 80 275 1.04 .98 100 4370 5710 102 112 244 254 0 2352 618 1734 .899 2310 1692 1.113 .887 -.154 -.173
14 2547 2496 360 682 2187 1814 2543 2455 387 747 2183 1773 0 0 614 878 184 479 98 94 98 79 4001 3956 1.206 .829 .812 .9 .83 .65 97 296 1 .97 110 4510 5700 100 111 257 268 0 2528 691 1837 .84 2486 1796 1.19 .823 -.252 -.282
15 1104 1354 375 651 729 703 1054 1320 390 732 679 669 0 0 353 650 176 469 98 66 87 30 1432 1348 1.037 .964 .985 1.4 1.15 1.24 86 274 1.21 .92 100 4670 5700 101 111 274 284 0 1371 659 712 .977 1337 678 1.024 .998 -.034 -.003
16 9751 10321 385 636 9366 9685 10021 10649 402 719 9636 10013 0 0 1744 2311 178 425 100 100 100 100 19051 19649 .967 1.034 1.039 1.03 1.08 .18 80 258 1.06 .99 100 4810 5710 102 112 288 298 0 10452 644 9808 1.047 10784 10140 .955 1.052 .067 .074
17 2537 2877 380 639 2157 2238 2548 2888 390 732 2168 2249 0 0 623 913 155 493 100 99 100 93 4395 4417 .964 1.038 1.037 1.09 1.02 .5 80 248 1.15 .98 100 4950 5710 102 112 302 312 0 2914 647 2266 1.051 2925 2278 .952 1.051 .071 .071
18 2915 3110 386 630 2529 2480 2895 3028 390 698 2509 2398 0 0 632 973 163 426 100 98 100 95 5009 4907 1.02 .981 .956 1.05 1.04 .45 97 269 1.09 .97 110 5090 5700 100 111 315 326 0 3150 638 2512 .993 3067 2429 1.007 .968 -.01 -.047
19 6888 7676 374 663 6514 7013 6680 7751 413 704 6306 7088 0 0 1445 1729 394 377 100 99 100 99 13527 13394 .929 1.077 1.124 1.09 1.12 .29 97 269 1.12 .99 110 5240 5700 100 111 330 341 0 7774 671 7102 1.09 7850 7178 .917 1.138 .125 .187
20 1884 1493 358 681 1526 812 1897 1496 401 717 1539 815 0 0 396 609 391 387 100 76 98 51 2338 2354 1.879 .532 .53 .64 .6 .39 86 284 .81 .95 100 5390 5700 101 111 346 356 0 1512 690 822 .539 1515 825 1.856 .536 -.892 -.899

Total number of rows: 41472

Table truncated, full table size 9690 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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