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Sample GSM741257 Query DataSets for GSM741257
Status Public on Nov 02, 2012
Title shfc41|HCT15
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 HCT15 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: HCT15
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/2006-06/68857.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
1 540 625 102 128 438 497 552 612 104 129 450 484 0 0 117 160 27 34 100 100 100 99 935 934 .881 1.135 1.076 1.16 1.14 .38 69 348 1.16 .98 90 2280 6640 79 88 87 96 0 702 144 558 1.275 688 544 .784 1.208 .35 .273
2 578 520 104 129 474 391 561 555 105 132 457 426 0 0 128 132 28 36 100 100 100 100 865 883 1.212 .825 .932 .83 .88 .28 60 300 .91 .98 80 2420 6640 80 88 102 110 0 584 145 439 .927 624 479 1.079 1.047 -.11 .067
3 925 1011 106 135 819 876 922 1029 109 135 816 894 0 0 258 289 28 38 100 100 100 100 1695 1710 .935 1.07 1.096 1.12 1.09 .42 60 319 1.1 .99 80 2560 6640 80 88 116 124 0 1136 152 984 1.202 1156 1004 .832 1.231 .265 .3
4 442 565 109 139 333 426 436 560 113 141 327 421 0 0 138 174 37 42 98 100 98 98 759 748 .782 1.279 1.287 1.44 1.3 .8 52 332 1.27 .99 80 2710 6640 80 88 131 139 0 635 156 479 1.437 629 473 .696 1.447 .523 .533
5 393 478 110 140 283 338 382 485 114 143 272 345 0 0 68 82 36 38 100 100 100 100 621 617 .837 1.194 1.268 1.24 1.19 .4 52 344 1.21 .99 80 2860 6640 80 88 146 154 0 537 157 380 1.342 545 388 .745 1.425 .424 .511
6 882 568 109 139 773 429 912 572 113 139 803 433 0 0 249 141 29 39 100 100 100 98 1202 1236 1.802 .555 .539 .57 .56 .18 52 334 .65 .98 80 3010 6640 80 88 161 169 0 638 156 482 .624 643 486 1.604 .606 -.681 -.723
7 308 364 106 140 202 224 300 371 108 139 194 231 0 0 87 93 28 41 98 94 96 90 426 425 .902 1.109 1.191 1.15 1.15 .56 52 319 1.18 .97 80 3150 6640 80 88 175 183 0 409 157 252 1.246 417 260 .803 1.338 .317 .42
8 843 579 103 140 740 439 800 574 107 142 697 434 0 0 223 130 30 37 100 100 100 100 1179 1131 1.686 .593 .623 .61 .61 .17 60 295 .69 .99 80 3290 6640 80 88 189 197 0 651 157 493 .667 645 488 1.5 .7 -.585 -.515
9 469 500 108 138 361 362 457 498 111 138 349 360 0 0 84 102 27 34 100 100 100 99 723 709 .997 1.003 1.032 1.02 .98 .33 97 263 1.08 .99 110 3440 6630 77 88 202 213 0 562 155 407 1.127 560 404 .888 1.159 .172 .213
10 857 1080 106 128 751 952 882 1113 108 133 776 985 0 0 162 190 27 35 100 100 99 100 1703 1761 .789 1.268 1.269 1.5 1.25 2.17 97 241 1.26 .99 110 3580 6630 77 88 216 227 0 1213 144 1070 1.424 1250 1107 .702 1.426 .51 .512
11 389 387 110 133 279 254 388 377 113 138 278 244 0 0 75 71 31 42 99 100 99 100 533 522 1.098 .91 .878 .94 .88 .37 86 238 1 .99 100 3730 6630 78 88 232 242 0 435 149 285 1.023 424 274 .978 .986 .033 -.02
12 390 414 113 135 277 279 389 426 113 141 276 291 0 0 105 126 33 44 99 95 99 91 556 567 .993 1.007 1.054 1.13 1.04 .73 146 215 1.07 .96 130 3880 6630 76 89 245 258 0 465 152 313 1.132 479 327 .884 1.185 .178 .244
13 534 672 100 130 434 542 540 690 104 132 440 560 0 0 115 139 29 36 100 100 100 100 976 1000 .801 1.249 1.273 1.28 1.25 .33 86 233 1.27 .99 100 4020 6630 78 88 261 271 0 755 146 609 1.403 775 629 .713 1.43 .489 .516
14 673 811 99 133 574 678 672 805 102 135 573 672 0 0 145 146 28 36 100 100 100 100 1252 1245 .847 1.181 1.173 1.27 1.22 .55 97 260 1.2 .99 110 4160 6630 77 88 274 285 0 911 149 762 1.327 904 755 .754 1.318 .408 .398
15 332 366 94 132 238 234 338 358 96 133 244 226 0 0 77 71 26 37 100 100 99 99 472 470 1.017 .983 .926 1.09 .98 .57 97 263 1.12 .98 110 4310 6630 77 88 289 300 0 411 148 263 1.105 402 254 .905 1.041 .144 .057
16 2418 2611 99 140 2319 2471 2497 2659 100 144 2398 2519 0 0 275 364 26 42 100 100 100 100 4790 4917 .938 1.066 1.05 1.06 1.08 .15 80 260 1.1 .99 100 4460 6630 78 88 305 315 0 2934 157 2776 1.197 2987 2830 .835 1.18 .26 .239
17 669 752 99 139 570 613 683 764 102 143 584 625 0 0 113 134 28 39 100 100 100 100 1183 1209 .93 1.075 1.07 1.1 1.03 .29 86 256 1.13 .99 100 4600 6630 78 88 319 329 0 845 156 689 1.208 858 702 .828 1.202 .273 .266
18 749 909 95 136 654 773 754 907 97 139 659 771 0 0 143 168 26 35 100 100 99 100 1427 1430 .846 1.182 1.17 1.35 1.19 1.66 97 241 1.21 .99 110 4750 6630 77 88 333 344 0 1021 153 868 1.328 1019 866 .753 1.314 .409 .394
19 1598 1786 95 137 1503 1649 1562 1739 97 141 1467 1602 0 0 359 379 25 42 100 100 100 100 3152 3069 .911 1.097 1.092 1.11 1.1 .19 86 245 1.12 .99 100 4890 6630 78 88 348 358 0 2007 154 1853 1.233 1954 1800 .811 1.227 .302 .295
20 566 560 95 130 471 430 571 553 97 138 476 423 0 0 94 117 26 43 100 99 100 99 901 899 1.095 .913 .889 .92 .93 .28 97 277 1 .99 110 5040 6620 76 87 362 373 0 629 146 483 1.026 621 475 .975 .998 .037 -.002

Total number of rows: 41472

Table truncated, full table size 8934 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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