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Sample GSM741252 Query DataSets for GSM741252
Status Public on Nov 02, 2012
Title shfc22|SW48
Sample type genomic
 
Channel 1
Source name Normal human female genomic DNA
Organism Homo sapiens
Characteristics reference: Normal human female genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SW48 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: SW48
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/2006-06/68864.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 1226 1591 208 399 1018 1192 1206 1479 215 485 998 1080 0 0 345 589 102 388 100 95 100 72 2210 2078 .854 1.171 1.082 1.28 1.12 .73 60 377 1.33 .95 80 2870 4980 62 70 83 91 0 1591 399 1192 1.171 1479 1080 .854 1.082 .227 .114
2 1403 1302 216 442 1187 860 1420 1241 228 518 1204 799 0 0 336 727 115 389 100 71 100 52 2047 2003 1.38 .725 .664 .88 .74 .7 52 358 .92 .94 80 3020 4980 62 70 98 106 0 1302 442 860 .724 1241 799 1.38 .664 -.465 -.592
3 2233 2934 208 403 2025 2531 2333 2860 223 480 2125 2457 0 0 652 1091 109 374 100 98 98 97 4556 4582 .8 1.25 1.156 1.45 1.3 1.18 60 357 1.32 .98 80 3160 4980 62 70 112 120 0 2934 403 2531 1.25 2860 2457 .8 1.156 .322 .209
4 1102 1642 221 416 881 1226 1053 1465 227 481 832 1049 0 0 437 918 110 366 95 86 91 68 2107 1881 .719 1.392 1.261 2.06 1.41 1.79 44 384 1.48 .89 70 3300 4980 62 69 126 133 0 1642 416 1226 1.391 1465 1049 .719 1.261 .477 .334
5 714 970 215 364 499 606 703 909 223 462 488 545 0 0 270 523 107 362 94 59 88 42 1105 1033 .823 1.214 1.117 1.57 1.27 1.83 69 373 1.36 .93 90 3450 4980 61 70 140 149 0 970 364 606 1.214 909 545 .824 1.117 .28 .159
6 2059 2818 200 422 1859 2396 2019 2846 217 481 1819 2424 0 0 642 1067 110 358 100 98 100 96 4255 4243 .776 1.289 1.333 1.39 1.33 .58 52 360 1.4 .98 80 3600 4980 62 70 156 164 0 2818 422 2396 1.289 2846 2424 .776 1.332 .366 .414
7 750 993 197 405 553 588 742 1003 214 468 545 598 0 0 328 532 108 358 92 64 83 44 1141 1143 .94 1.063 1.097 1.41 1.05 1.3 36 360 1.4 .95 70 3750 4980 62 69 171 178 0 993 405 588 1.063 1003 598 .941 1.097 .088 .134
8 1748 2227 195 404 1553 1823 1796 2025 212 469 1601 1621 0 0 528 999 110 379 100 95 98 90 3376 3222 .852 1.174 1.012 1.3 1.09 1.01 60 313 1.28 .98 80 3890 4980 62 70 185 193 0 2227 404 1823 1.174 2025 1621 .852 1.012 .231 .018
9 1135 1494 210 396 925 1098 1105 1429 230 470 895 1033 0 0 350 696 121 385 100 88 98 64 2023 1928 .842 1.187 1.154 1.34 1.23 .91 97 279 1.32 .95 110 4030 4980 60 71 197 208 0 1494 396 1098 1.187 1429 1033 .843 1.154 .247 .207
10 2320 2662 221 344 2099 2318 2330 2659 228 438 2109 2315 0 0 456 746 111 350 100 100 100 100 4417 4424 .906 1.104 1.098 1.13 1.11 .4 80 250 1.16 .98 100 4180 4980 61 71 213 223 0 2662 344 2318 1.104 2659 2315 .906 1.098 .143 .134
11 1104 1220 244 334 860 886 1111 1138 253 418 867 804 0 0 327 611 116 340 100 80 98 58 1746 1671 .971 1.03 .927 1.21 1.09 1.14 86 280 1.14 .95 100 4320 4980 61 71 227 237 0 1220 334 886 1.03 1138 804 .971 .927 .043 -.109
12 1575 1866 250 298 1325 1568 1515 1690 270 390 1265 1392 0 0 373 741 133 338 100 99 100 93 2893 2657 .845 1.183 1.1 1.3 1.18 .8 70 311 1.19 .97 90 4470 4980 61 70 242 251 0 1866 298 1568 1.183 1690 1392 .845 1.1 .243 .138
13 1653 1921 233 337 1420 1584 1652 1798 256 414 1419 1461 0 0 423 924 127 355 99 91 99 83 3004 2880 .896 1.115 1.03 1.25 1.05 .82 70 291 1.18 .96 90 4620 4980 61 70 257 266 0 1921 337 1584 1.115 1798 1461 .897 1.029 .158 .042
14 2020 2731 230 384 1790 2347 2024 2674 246 455 1794 2290 0 0 423 908 116 363 100 100 100 96 4137 4084 .763 1.311 1.276 1.37 1.25 .61 80 272 1.36 .98 100 4760 4980 61 71 271 281 0 2731 384 2347 1.311 2674 2290 .763 1.276 .391 .352
15 1020 1204 252 385 768 819 967 1091 258 442 715 706 0 0 288 646 119 325 100 79 99 54 1587 1421 .938 1.066 .987 1.28 1.11 .91 80 292 1.18 .93 100 4910 4980 61 71 286 296 0 1204 385 819 1.066 1091 706 .938 .987 .093 -.018
16 6464 8584 234 368 6230 8216 6684 8875 252 441 6450 8507 0 0 1358 2343 117 334 100 100 100 100 14446 14957 .758 1.319 1.319 1.32 1.35 .32 80 286 1.34 .99 100 5060 4980 61 71 301 311 0 8583 368 8215 1.319 8874 8506 .758 1.319 .399 .399
17 2282 2668 230 354 2052 2314 2219 2555 247 414 1989 2201 0 0 445 1007 127 311 100 97 100 97 4366 4190 .887 1.128 1.107 1.17 1.06 .58 70 273 1.18 .98 90 5200 4980 61 70 315 324 0 2668 354 2314 1.128 2555 2201 .887 1.106 .173 .146
18 2336 2978 227 393 2109 2585 2370 2946 246 463 2143 2553 0 0 491 1062 127 335 100 100 100 99 4694 4696 .816 1.226 1.191 1.29 1.18 .65 86 272 1.28 .96 100 5340 4980 61 71 329 339 0 2978 393 2585 1.226 2946 2553 .816 1.191 .293 .252
19 5861 6994 215 384 5646 6610 5914 7031 232 452 5699 6647 0 0 914 1772 122 342 100 100 100 100 12256 12346 .854 1.171 1.166 1.17 1.18 .29 86 281 1.2 .99 100 5490 4980 61 71 344 354 0 6993 384 6609 1.171 7030 6646 .854 1.166 .227 .222
20 1756 1850 205 358 1551 1492 1783 1775 217 406 1578 1417 0 0 404 856 111 321 100 95 100 88 3043 2995 1.04 .962 .898 1.03 .9 .62 86 285 1.09 .95 100 5640 4980 61 71 359 369 0 1850 358 1492 .962 1775 1417 1.04 .898 -.056 -.155

Total number of rows: 41472

Table truncated, full table size 9549 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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