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Sample GSM741255 Query DataSets for GSM741255
Status Public on Nov 02, 2012
Title shgu230|T84
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 T84 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: T84
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/2006-08/69846.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 GPL7780
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
1 942 549 362 399 580 150 908 566 374 406 546 167 0 0 278 146 128 150 95 57 90 17 730 713 3.867 .259 .306 .39 .34 .35 86 345 .6 .91 100 2690 6130 40 50 32 42 0 386 281 106 .182 398 118 5.492 .215 -2.457 -2.215
2 2093 2172 362 400 1731 1772 2143 2256 393 428 1781 1856 0 0 477 428 186 230 100 100 100 98 3503 3637 .977 1.024 1.042 1.09 1.05 .42 61 302 1.05 .99 90 2830 6140 41 50 46 55 0 1529 282 1247 .721 1588 1307 1.388 .734 -.473 -.447
3 2327 2484 374 405 1953 2079 1664 1369 409 444 1290 964 0 0 6012 7336 272 307 100 98 100 86 4032 2254 .939 1.065 .747 1.2 .78 2.91 80 306 1.07 .97 100 2980 6140 41 51 61 71 0 1749 285 1464 .749 964 679 1.334 .526 -.416 -.927
4 2119 2213 375 393 1744 1820 2129 2358 375 397 1754 1965 0 0 508 586 100 111 100 98 100 97 3564 3719 .958 1.044 1.12 1.05 1.06 .32 58 339 1.06 .99 80 3120 6150 43 51 76 84 0 1558 277 1281 .735 1660 1383 1.361 .789 -.445 -.342
5 1813 1361 362 378 1451 983 1782 1356 370 387 1420 978 0 0 375 269 98 112 100 100 100 100 2434 2398 1.476 .677 .689 .7 .69 .22 80 325 .75 .98 100 3270 6140 41 51 90 100 0 958 266 692 .477 955 689 2.097 .485 -1.068 -1.044
6 2106 2197 360 378 1746 1819 2193 2274 374 388 1833 1896 0 0 405 447 103 108 100 100 100 100 3565 3729 .96 1.042 1.034 1.06 1.09 .3 48 306 1.05 .99 80 3420 6150 43 51 106 114 0 1547 266 1281 .733 1601 1335 1.363 .728 -.447 -.458
7 2046 1528 366 389 1680 1139 2085 1527 383 396 1719 1138 0 0 419 324 118 106 100 100 100 100 2819 2857 1.475 .678 .662 .69 .69 .2 136 217 .75 .99 130 3570 6140 39 52 118 131 0 1076 274 802 .477 1075 801 2.095 .466 -1.067 -1.101
8 1752 2288 371 381 1381 1907 1726 2274 389 383 1355 1893 0 0 336 349 122 108 100 100 100 100 3288 3248 .724 1.381 1.397 1.46 1.41 .49 97 224 1.31 .99 110 3700 6140 40 51 132 143 0 1611 268 1343 .972 1601 1333 1.029 .984 -.041 -.024
9 1714 2454 371 391 1343 2063 1738 2451 381 392 1367 2060 0 0 352 446 103 114 100 100 100 100 3406 3427 .651 1.536 1.507 1.61 1.56 .45 86 260 1.43 .99 100 3850 6140 41 51 148 158 0 1728 275 1452 1.081 1726 1450 .925 1.061 .113 .085
10 2879 2776 376 379 2503 2397 2949 2920 387 388 2573 2541 0 0 890 716 105 115 100 100 98 98 4900 5114 1.044 .958 .988 1.03 1.02 .41 64 288 .96 .99 90 4000 6140 41 50 163 172 0 1954 267 1688 .674 2056 1789 1.483 .695 -.569 -.524
11 1220 1390 396 379 824 1011 1198 1359 401 386 802 980 0 0 283 266 115 122 100 100 100 100 1835 1782 .815 1.227 1.222 1.35 1.22 .58 86 339 1.15 .98 100 4140 6140 41 51 177 187 0 979 267 712 .864 957 690 1.158 .86 -.211 -.217
12 932 752 386 379 546 373 936 732 397 384 550 353 0 0 359 287 116 123 85 76 72 61 919 903 1.464 .683 .642 .83 .7 .65 72 315 .8 .98 90 4300 6140 41 50 193 202 0 529 267 263 .481 515 249 2.079 .452 -1.056 -1.146
13 1723 3158 393 389 1330 2769 1681 3171 404 404 1288 2782 0 0 385 500 117 130 100 100 100 100 4099 4070 .48 2.082 2.16 2.21 2.17 .64 97 312 1.82 .99 110 4430 6140 40 51 205 216 0 2223 274 1949 1.466 2232 1959 .682 1.521 .552 .605
14 2552 2296 396 386 2156 1910 2576 2330 411 407 2180 1944 0 0 379 377 120 136 100 100 100 100 4066 4124 1.129 .886 .892 .89 .89 .18 86 269 .9 .99 100 4580 6140 41 51 221 231 0 1616 272 1345 .624 1640 1369 1.603 .628 -.681 -.672
15 1204 1869 385 361 819 1508 1170 1868 397 389 785 1507 0 0 275 315 117 200 99 99 99 99 2327 2292 .543 1.841 1.92 2.16 1.92 1.96 156 180 1.55 .98 140 4720 6150 40 54 233 247 0 1316 254 1062 1.296 1315 1061 .771 1.352 .374 .435
16 4269 6999 398 385 3871 6614 4251 7043 404 400 3853 6658 0 0 849 944 108 127 100 100 100 100 10485 10511 .585 1.709 1.728 1.76 1.72 .33 115 223 1.64 .99 120 4870 6150 41 53 249 261 0 4927 271 4656 1.203 4958 4687 .831 1.217 .266 .283
17 1784 3227 392 398 1392 2829 1738 3234 396 404 1346 2836 0 0 437 672 103 121 100 100 100 100 4221 4182 .492 2.032 2.107 2.14 2 .63 86 257 1.79 .99 100 5020 6140 41 51 265 275 0 2272 280 1992 1.431 2277 1997 .699 1.483 .517 .569
18 2044 3526 385 386 1659 3140 2091 3651 400 396 1706 3265 0 0 533 810 126 118 100 100 99 100 4799 4971 .528 1.893 1.914 1.98 1.96 .5 72 283 1.71 .99 90 5170 6140 41 50 280 289 0 2482 272 2211 1.332 2570 2299 .75 1.347 .414 .43
19 4574 8665 375 380 4199 8285 4573 8851 399 392 4198 8471 0 0 1114 1671 119 114 100 100 100 100 12484 12669 .507 1.973 2.018 2.03 2 .35 80 294 1.89 1 100 5310 6150 42 52 294 304 0 6100 268 5833 1.389 6231 5964 .72 1.421 .474 .506
20 2042 2450 366 376 1676 2074 2032 2620 381 388 1666 2244 0 0 408 588 99 108 100 100 100 100 3750 3910 .808 1.237 1.347 1.23 1.25 .3 44 363 1.2 .99 70 5460 6160 44 51 310 317 0 1725 265 1460 .871 1844 1580 1.148 .948 -.199 -.077

Total number of rows: 41472

Table truncated, full table size 9457 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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