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Sample GSM741249 Query DataSets for GSM741249
Status Public on Nov 02, 2012
Title shgu234|COLO205
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 COLO205 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: COLO205
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/2006-08/69652.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 3667 2765 496 516 3171 2249 3509 2737 543 556 3013 2221 0 0 1345 815 350 303 100 100 100 98 5420 5234 1.41 .709 .737 .73 .72 .24 97 298 .75 .99 110 2660 6570 39 50 36 47 0 2655 496 2160 .681 2629 2133 1.468 .708 -.554 -.498
2 4579 4315 500 481 4079 3834 4774 4633 601 564 4274 4152 0 0 1538 1538 584 423 96 99 93 94 7913 8426 1.064 .94 .971 .96 .94 .31 72 244 .95 .99 90 2810 6580 41 50 52 61 0 4144 462 3682 .903 4449 3987 1.108 .933 -.148 -.1
3 4784 3423 494 456 4290 2967 4878 3330 515 485 4384 2874 0 0 1228 919 259 245 99 100 99 100 7257 7258 1.446 .692 .656 .7 .68 .19 97 255 .72 .99 110 2950 6580 40 51 65 76 0 3287 438 2849 .664 3198 2760 1.506 .63 -.59 -.668
4 3923 3744 487 445 3436 3299 4102 3438 498 479 3615 2993 0 0 1395 2648 175 226 96 100 93 94 6735 6608 1.042 .96 .828 1.73 .86 3.83 69 288 .95 .88 90 3090 6590 42 51 80 89 0 3596 427 3168 .922 3302 2874 1.085 .795 -.117 -.331
5 2984 1783 483 475 2501 1308 3043 1766 494 501 2560 1291 0 0 797 534 163 226 99 98 99 95 3809 3851 1.912 .523 .504 .67 .53 1.17 86 297 .6 .99 100 3250 6580 41 51 96 106 0 1712 456 1256 .502 1696 1240 1.991 .484 -.993 -1.046
6 3677 3090 486 477 3191 2613 3652 3122 490 515 3166 2645 0 0 1261 1122 156 234 100 100 98 98 5804 5811 1.221 .819 .835 .92 .81 .81 48 330 .85 .98 80 3400 6580 42 50 112 120 0 2968 458 2509 .786 2998 2540 1.272 .802 -.347 -.318
7 3764 2954 481 477 3283 2477 3696 2969 494 510 3215 2492 0 0 871 672 182 215 100 100 100 99 5760 5707 1.325 .754 .775 .77 .79 .24 136 216 .79 .99 130 3550 6580 39 52 124 137 0 2837 458 2379 .725 2851 2393 1.38 .744 -.465 -.426
8 3162 3160 467 465 2695 2695 3119 3093 555 492 2652 2628 0 0 683 899 855 333 100 100 91 100 5390 5280 1 1 .991 1.03 .96 .38 97 205 1.01 .98 110 3680 6580 40 51 138 149 0 3035 447 2588 .96 2970 2524 1.041 .952 -.058 -.071
9 2946 2795 495 473 2451 2322 2940 2802 513 498 2445 2329 0 0 730 764 201 231 100 99 99 99 4773 4774 1.056 .947 .953 1 .97 .37 97 229 .94 .98 110 3830 6580 40 51 153 164 0 2684 454 2230 .91 2691 2237 1.099 .915 -.136 -.128
10 6218 5419 485 484 5733 4935 5871 5425 546 521 5386 4941 0 0 1622 1245 740 338 100 100 100 100 10668 10327 1.162 .861 .917 .88 .88 .21 64 247 .87 .99 90 3980 6580 41 50 169 178 0 5204 465 4739 .827 5210 4745 1.21 .881 -.275 -.183
11 2173 2400 474 528 1699 1872 2213 2460 549 564 1739 1932 0 0 596 646 686 353 97 100 73 97 3571 3671 .908 1.102 1.111 1.2 1.09 .59 104 301 1.11 .98 110 4120 6570 39 50 182 193 0 2305 507 1798 1.058 2362 1855 .945 1.067 .082 .093
12 2461 2298 470 478 1991 1820 2767 2487 493 506 2297 2009 0 0 1305 1090 181 220 86 86 84 81 3811 4306 1.094 .914 .875 1.57 .92 3.72 37 334 .92 .99 70 4270 6570 41 48 199 206 -50 2207 459 1748 .878 2388 1929 1.139 .84 -.188 -.252
13 3837 4565 471 489 3366 4076 3706 4570 537 507 3235 4081 0 0 1066 1236 798 246 100 100 98 100 7442 7316 .826 1.211 1.262 1.24 1.22 .34 97 277 1.19 .99 110 4410 6580 40 51 211 222 0 4384 470 3914 1.163 4389 3919 .86 1.212 .218 .277
14 4978 4122 481 489 4497 3633 4896 4121 646 524 4415 3632 0 0 1054 905 1705 270 100 100 91 100 8130 8047 1.238 .808 .823 .82 .8 .22 86 215 .83 .99 100 4560 6580 41 51 227 237 0 3959 470 3489 .776 3958 3488 1.289 .79 -.366 -.34
15 2235 2020 458 424 1777 1596 2216 1934 460 471 1758 1510 0 0 550 581 188 249 99 99 98 98 3373 3268 1.113 .898 .859 .95 .88 .43 176 157 .9 .98 150 4700 6580 38 53 238 253 0 1940 407 1533 .863 1857 1450 1.159 .825 -.213 -.278
16 9674 11896 438 476 9236 11420 9530 11607 473 503 9092 11131 0 0 4182 4466 186 245 99 100 98 100 20656 20223 .809 1.236 1.224 1.55 1.23 2.7 124 167 1.22 .99 120 4850 6590 41 53 255 267 0 11424 457 10967 1.187 11147 10690 .842 1.176 .248 .234
17 4605 5199 461 474 4144 4725 3552 4269 491 496 3091 3795 1 0 6699 5350 164 229 100 100 100 100 8869 6886 .877 1.14 1.228 1.27 1.22 .44 97 219 1.13 .98 110 4990 6580 40 51 269 280 0 4993 455 4538 1.095 4100 3645 .913 1.179 .131 .238
18 5052 5946 454 465 4598 5481 4673 6242 487 496 4219 5777 0 0 4987 3945 170 230 96 96 93 95 10079 9996 .839 1.192 1.369 1.63 1.35 2.04 84 250 1.15 .94 100 5140 6590 42 52 285 295 0 5710 447 5264 1.145 5995 5548 .874 1.315 .195 .395
19 9244 10832 453 443 8791 10389 9351 10936 479 482 8898 10493 0 0 1619 1773 179 225 100 100 100 100 19180 19391 .846 1.182 1.179 1.19 1.16 .17 79 292 1.18 .99 100 5280 6580 41 51 299 309 0 10403 425 9977 1.135 10503 10077 .881 1.133 .183 .18
20 3118 3168 447 455 2671 2713 3145 3151 472 486 2698 2696 0 0 691 872 173 230 100 100 100 100 5384 5394 .985 1.016 .999 1.02 1 .31 52 361 1.03 .99 80 5440 6590 43 51 316 324 0 3042 437 2605 .975 3026 2589 1.025 .96 -.036 -.059

Total number of rows: 41472

Table truncated, full table size 9633 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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