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Sample GSM741251 Query DataSets for GSM741251
Status Public on Nov 02, 2012
Title shfc38|SKCO1
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 SKCO1 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: SKCO1
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/2006-07/69145.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 1578 1478 253 265 1325 1213 1560 1373 278 322 1307 1108 0 0 391 762 143 277 100 90 100 81 2538 2415 1.092 .915 .848 1.01 .82 .76 69 372 .95 .96 90 3010 6180 65 74 72 81 0 1474 264 1210 .913 1370 1105 1.095 .846 -.131 -.242
2 1638 1291 244 264 1394 1027 1653 1188 262 339 1409 924 0 0 396 736 139 298 100 88 100 70 2421 2333 1.357 .737 .656 .78 .71 .52 60 322 .8 .94 80 3160 6180 66 74 88 96 0 1288 263 1024 .735 1185 922 1.361 .654 -.444 -.612
3 2530 2685 235 262 2295 2423 2535 2595 245 347 2300 2333 0 0 609 954 112 326 100 100 100 98 4718 4633 .947 1.056 1.014 1.1 1.06 .48 60 333 1.06 .98 80 3300 6180 66 74 102 110 0 2678 261 2417 1.053 2588 2327 .95 1.012 .075 .017
4 1408 1588 230 299 1178 1289 1255 1561 256 342 1025 1262 0 0 604 879 264 280 96 88 87 73 2467 2287 .914 1.094 1.231 1.17 .94 .8 52 339 1.16 .98 80 3460 6180 66 74 118 126 0 1584 298 1286 1.091 1557 1259 .916 1.228 .126 .296
5 971 1121 231 315 740 806 955 1098 262 356 724 783 0 0 282 577 266 275 97 83 77 62 1546 1507 .918 1.089 1.081 1.27 .98 1.08 60 331 1.18 .95 80 3600 6180 66 74 132 140 0 1118 314 804 1.086 1095 781 .92 1.079 .12 .109
6 2408 2232 229 291 2179 1941 2532 2160 244 359 2303 1869 0 0 675 954 113 290 100 96 98 92 4120 4172 1.123 .891 .812 .94 .85 .52 52 338 .93 .98 80 3750 6180 66 74 147 155 0 2226 290 1936 .889 2155 1864 1.125 .81 -.171 -.305
7 948 1235 231 274 717 961 922 1159 238 359 691 885 0 0 237 729 102 290 100 86 100 70 1678 1576 .746 1.34 1.281 1.54 1.16 1.21 37 384 1.29 .92 70 3890 6170 65 72 161 168 0 1232 273 959 1.337 1156 883 .748 1.278 .419 .353
8 1894 1599 239 288 1655 1311 1952 1542 250 369 1713 1254 0 0 476 787 109 305 100 92 100 82 2966 2967 1.262 .792 .732 .86 .78 .46 60 298 .83 .97 80 4030 6180 66 74 175 183 0 1595 287 1308 .79 1538 1251 1.266 .73 -.34 -.454
9 1135 1117 224 248 911 869 1125 1029 235 343 901 781 0 0 297 577 104 310 99 89 99 62 1780 1682 1.048 .954 .867 1.08 .89 .99 97 268 1 .94 110 4170 6170 63 74 187 198 0 1114 247 867 .951 1026 779 1.051 .865 -.072 -.21
10 2351 2056 222 281 2129 1775 2335 2009 232 378 2113 1728 0 0 494 830 104 349 100 97 100 92 3904 3841 1.199 .834 .818 .87 .8 .46 97 254 .88 .96 110 4320 6170 63 74 202 213 0 2051 280 1771 .832 2004 1724 1.202 .816 -.266 -.294
11 955 826 220 273 735 553 903 791 239 367 683 518 0 0 311 391 112 338 99 73 98 37 1288 1201 1.329 .752 .758 .98 .84 .74 97 258 .88 .95 110 4470 6170 63 74 217 228 0 824 272 552 .75 789 517 1.332 .757 -.414 -.403
12 1381 1492 220 269 1161 1223 1420 1443 237 352 1200 1174 0 0 427 737 111 308 100 90 98 78 2384 2374 .949 1.053 .978 1.43 1.04 1.67 86 262 1.07 .95 100 4610 6180 65 75 232 242 0 1488 268 1220 1.051 1439 1171 .952 .976 .071 -.035
13 1364 1357 227 273 1137 1084 1382 1252 235 352 1155 979 0 0 429 696 116 300 99 94 99 67 2221 2134 1.049 .953 .848 1.06 .89 .89 86 265 1.02 .96 100 4760 6180 65 75 247 257 0 1354 272 1081 .951 1249 977 1.052 .845 -.073 -.242
14 1824 1702 205 290 1619 1412 1883 1565 219 357 1678 1275 0 0 403 749 107 287 100 96 100 94 3031 2953 1.147 .872 .76 .94 .85 .59 97 278 .95 .96 110 4900 6170 63 74 260 271 0 1698 289 1408 .87 1561 1272 1.149 .758 -.201 -.4
15 918 1065 210 288 708 777 939 1003 228 362 729 715 0 0 317 528 106 295 98 82 97 61 1485 1444 .911 1.097 .981 1.49 1.16 1.92 97 278 1.19 .92 110 5050 6170 63 74 275 286 0 1062 287 775 1.095 1000 713 .913 .978 .131 -.032
16 6965 7570 227 286 6738 7284 6931 7384 244 372 6704 7098 0 0 852 1975 112 323 100 100 100 100 14022 13802 .925 1.081 1.059 1.08 1.06 .3 70 299 1.09 .99 90 5200 6170 64 73 291 300 0 7551 285 7266 1.078 7365 7080 .927 1.056 .109 .079
17 2058 2257 233 339 1825 1918 1994 2171 392 442 1761 1832 0 0 516 843 1666 450 56 99 0 86 3743 3593 .952 1.051 1.04 1.12 1.02 .59 80 264 1.13 .96 100 5350 6170 64 74 306 316 0 2251 338 1913 1.048 2166 1827 .954 1.038 .068 .053
18 1890 1842 211 308 1679 1534 1888 1534 316 420 1677 1226 0 0 460 913 1385 392 77 95 1 80 3213 2903 1.095 .914 .731 .96 .92 .6 97 253 1.01 .95 110 5490 6170 63 74 319 330 0 1837 307 1530 .911 1530 1223 1.097 .729 -.134 -.456
19 5502 6727 200 300 5302 6427 5379 6604 221 393 5179 6304 0 0 1014 1790 107 343 100 100 100 100 11729 11483 .825 1.212 1.217 1.22 1.22 .33 97 257 1.24 .99 110 5630 6170 63 74 333 344 0 6710 299 6411 1.209 6587 6288 .827 1.214 .274 .28
20 1517 1016 203 305 1314 711 1509 919 221 377 1306 614 0 0 369 488 111 313 100 79 100 49 2025 1920 1.848 .541 .47 .6 .49 .43 97 271 .68 .96 110 5780 6170 63 74 348 359 0 1013 304 709 .54 917 612 1.853 .469 -.89 -1.092

Total number of rows: 41472

Table truncated, full table size 9538 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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