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Sample GSM741268 Query DataSets for GSM741268
Status Public on Nov 02, 2012
Title shfc42|LOVO
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 LOVO genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: LOVO
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol model: GenePix 4000A
Description Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68858.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
1 422 438 129 106 293 332 434 457 133 109 305 351 0 0 86 138 31 33 100 100 100 96 625 656 .883 1.133 1.151 1.2 1.16 .7 69 356 1.05 .97 90 2140 6610 100 109 73 82 0 437 106 331 1.131 456 350 .884 1.149 .178 .2
2 504 364 130 105 374 259 537 389 132 107 407 284 0 0 125 127 31 32 100 98 100 95 633 691 1.444 .693 .698 .71 .68 .35 60 316 .74 .96 80 2280 6610 101 109 88 96 0 363 105 259 .691 388 284 1.446 .697 -.533 -.522
3 846 870 132 109 714 761 860 918 133 113 728 809 0 0 243 272 31 34 98 98 98 98 1475 1537 .938 1.066 1.111 1.65 1.08 4.02 60 332 1.03 .97 80 2430 6610 101 109 103 111 0 869 109 760 1.064 916 808 .94 1.109 .09 .15
4 546 257 125 109 421 148 514 244 128 109 389 135 0 0 128 80 31 34 100 95 100 93 569 524 2.845 .352 .347 .35 .33 .19 44 351 .48 .97 70 2570 6610 101 108 117 124 0 257 109 148 .351 244 135 2.849 .346 -1.511 -1.529
5 312 317 124 101 188 216 322 338 126 106 198 237 0 0 85 111 31 35 97 91 97 89 404 435 .87 1.149 1.197 1.24 1.1 .75 64 328 1.02 .97 90 2720 6610 100 109 131 140 0 316 101 216 1.147 337 237 .872 1.195 .198 .257
6 721 779 129 108 592 671 735 842 131 111 606 734 0 0 184 273 29 32 100 98 100 92 1263 1340 .882 1.133 1.211 1.12 1.18 .43 52 325 1.1 .98 80 2870 6610 101 109 147 155 0 778 108 670 1.132 841 733 .884 1.209 .178 .274
7 283 294 128 101 155 193 285 294 129 102 157 193 0 0 78 100 31 30 98 96 87 90 348 350 .803 1.245 1.229 1.5 1.35 1.19 52 317 1.04 .95 80 3010 6610 101 109 161 169 0 294 101 193 1.243 294 193 .804 1.227 .314 .295
8 640 691 122 99 518 592 647 680 125 102 525 581 0 0 144 199 33 31 100 100 100 100 1110 1106 .875 1.143 1.107 1.18 1.09 .45 60 298 1.07 .98 80 3150 6610 101 109 175 183 0 690 99 591 1.141 679 580 .876 1.105 .19 .144
9 404 391 124 101 280 290 404 402 126 103 280 301 0 0 67 87 31 30 100 99 100 99 570 581 .966 1.036 1.075 1.07 1.08 .38 97 271 .98 .98 110 3300 6600 98 109 188 199 0 390 101 290 1.034 401 300 .967 1.073 .048 .102
10 678 963 117 89 561 874 686 960 120 91 569 871 0 0 141 170 30 27 100 100 99 100 1435 1440 .642 1.558 1.531 1.71 1.59 1.06 86 230 1.41 .99 100 3440 6610 100 110 203 213 0 961 89 873 1.555 958 870 .643 1.528 .637 .612
11 330 291 116 82 214 209 332 304 118 87 216 222 0 0 63 73 28 37 100 98 98 94 423 438 1.024 .977 1.028 1.12 .94 1.03 97 258 .87 .98 110 3590 6600 98 109 217 228 0 291 82 209 .975 303 222 1.026 1.026 -.037 .037
12 9920 3306 120 88 9800 3218 10168 3456 128 105 10048 3368 0 0 6912 2885 47 77 100 100 100 100 13018 13416 3.045 .328 .335 .61 .3 .84 80 274 .33 .94 100 3740 6600 99 109 233 243 0 3300 88 3213 .328 3450 3362 3.051 .335 -1.609 -1.579
13 456 524 117 96 339 428 478 545 126 108 361 449 0 0 114 111 48 71 96 100 93 98 767 810 .792 1.263 1.244 1.77 1.19 2.44 80 261 1.13 .98 100 3890 6610 100 110 248 258 0 523 96 427 1.26 544 448 .793 1.242 .334 .312
14 603 699 114 101 489 598 613 720 115 103 499 619 0 0 118 126 28 32 100 100 100 100 1087 1118 .818 1.223 1.24 1.29 1.23 .53 97 266 1.16 .99 110 4030 6600 98 109 261 272 0 698 101 597 1.221 719 618 .819 1.238 .288 .308
15 307 335 111 101 196 234 314 324 113 105 203 223 0 0 83 76 29 32 96 100 96 99 430 426 .838 1.194 1.099 1.72 1.23 2.93 96 235 1.08 .98 110 4180 6610 99 110 276 287 0 334 101 234 1.192 323 223 .839 1.097 .253 .133
16 1893 2426 111 101 1782 2325 2052 2527 112 106 1941 2426 0 0 580 483 29 34 100 100 99 100 4107 4367 .766 1.305 1.25 1.83 1.27 2.42 86 246 1.26 .99 100 4320 6610 100 110 291 301 0 2422 101 2321 1.302 2523 2422 .768 1.248 .381 .319
17 641 770 110 108 531 662 654 778 112 109 544 670 0 0 107 163 29 32 100 100 100 100 1193 1214 .802 1.247 1.232 1.26 1.27 .31 80 250 1.2 .99 100 4470 6600 99 109 306 316 0 769 108 661 1.245 777 669 .803 1.23 .316 .298
18 699 870 111 105 588 765 727 874 113 104 616 769 0 0 152 169 30 29 100 100 99 100 1353 1385 .769 1.301 1.248 1.51 1.3 1.27 97 245 1.24 .99 110 4610 6600 98 109 319 330 0 869 105 764 1.299 873 768 .77 1.246 .377 .318
19 1700 2307 106 104 1594 2203 1776 2369 110 107 1670 2265 0 0 463 506 29 29 100 100 100 100 3797 3935 .724 1.382 1.356 1.6 1.39 1.2 97 237 1.35 .99 110 4760 6600 98 109 334 345 0 2303 104 2199 1.38 2365 2261 .725 1.354 .464 .437
20 529 595 105 99 424 496 542 593 107 103 437 494 0 0 120 108 29 33 99 100 97 100 920 931 .855 1.17 1.13 1.44 1.15 1.46 97 253 1.12 .99 110 4900 6600 98 109 348 359 0 594 99 495 1.168 592 493 .856 1.129 .224 .174

Total number of rows: 41472

Table truncated, full table size 9086 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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