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Sample GSM741260 Query DataSets for GSM741260
Status Public on Nov 02, 2012
Title shgu229|HCA7
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 HCA7 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: HCA7
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/2006-08/69845.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 2598 1543 469 331 2129 1212 2547 1574 494 363 2078 1243 0 0 454 343 187 217 100 100 100 99 3341 3321 1.757 .569 .598 .58 .58 .18 80 348 .6 .99 100 2600 5840 27 37 27 37 0 1151 247 904 .425 1174 927 2.355 .446 -1.236 -1.164
2 3095 2425 479 338 2616 2087 3286 2498 539 427 2807 2160 0 0 870 663 332 438 97 100 93 91 4703 4967 1.253 .798 .77 .92 .78 .65 58 314 .79 .99 80 2740 5850 29 37 42 50 0 1809 252 1557 .595 1863 1611 1.681 .574 -.749 -.801
3 3922 3932 472 333 3450 3599 3810 3831 473 341 3338 3498 0 0 875 852 147 126 100 100 100 100 7049 6836 .959 1.043 1.048 1.06 1.05 .22 80 298 1.01 .99 100 2890 5850 28 38 56 66 0 2933 248 2684 .778 2857 2609 1.285 .782 -.362 -.356
4 2980 2687 467 342 2513 2345 3245 2894 482 356 2778 2552 0 0 1030 896 146 134 95 100 93 98 4858 5330 1.072 .933 .919 1.16 .93 1.38 61 335 .9 .99 90 3030 5850 28 37 70 79 0 2004 255 1749 .696 2158 1903 1.437 .685 -.523 -.545
5 3221 2497 468 330 2753 2167 3207 2583 478 341 2739 2253 0 0 720 476 149 117 100 100 100 100 4920 4992 1.27 .787 .823 .84 .82 .31 70 350 .77 .99 90 3180 5850 28 37 85 94 0 1862 246 1616 .587 1927 1680 1.703 .614 -.768 -.705
6 2917 2534 470 338 2447 2196 3012 2596 482 351 2542 2258 0 0 923 924 150 119 98 100 98 98 4643 4800 1.114 .897 .888 .9 .9 .28 51 305 .87 .99 80 3330 5850 29 37 101 109 0 1890 252 1638 .669 1936 1684 1.494 .663 -.579 -.594
7 3382 3168 445 336 2937 2832 3230 3077 475 345 2785 2741 0 0 2016 969 193 109 100 100 100 100 5769 5526 1.037 .964 .984 1.02 .98 .3 136 219 .94 .97 130 3480 5850 26 39 113 126 0 2363 251 2112 .719 2295 2044 1.39 .734 -.476 -.446
8 2838 2975 434 332 2404 2643 2669 2863 611 377 2235 2531 0 0 1386 1093 2051 233 66 100 1 100 5047 4766 .91 1.099 1.132 1.19 1.16 .56 86 222 1.05 .97 100 3620 5850 28 38 129 139 0 2219 248 1971 .82 2135 1888 1.22 .845 -.286 -.244
9 2642 2942 413 337 2229 2605 2594 3000 544 368 2181 2663 0 0 581 536 1850 211 74 100 1 100 4834 4844 .856 1.169 1.221 1.2 1.18 .3 80 273 1.12 .99 100 3770 5850 28 38 144 154 0 2194 251 1943 .872 2238 1986 1.147 .911 -.198 -.135
10 4377 4478 399 326 3978 4152 4341 4652 412 338 3942 4326 0 0 1023 888 135 123 100 100 100 100 8130 8268 .958 1.044 1.097 1.06 1.06 .2 61 280 1.03 .99 90 3910 5840 27 36 158 167 0 3340 243 3097 .778 3470 3227 1.285 .818 -.361 -.289
11 2570 2945 405 326 2165 2619 2529 2936 413 330 2124 2610 0 0 565 456 142 120 100 100 100 100 4784 4734 .827 1.21 1.229 1.27 1.27 .4 97 317 1.15 .99 110 4050 5840 26 37 171 182 0 2197 243 1953 .902 2190 1947 1.108 .916 -.148 -.126
12 2550 2513 434 319 2116 2194 2556 2615 450 340 2122 2296 0 0 559 614 140 143 100 100 100 100 4310 4418 .964 1.037 1.082 1.08 1 .38 44 293 .99 .98 70 4210 5860 30 37 189 196 0 1874 238 1636 .773 1950 1712 1.293 .807 -.371 -.309
13 1908 2579 440 325 1468 2254 1864 2588 455 347 1424 2263 0 0 547 684 145 144 98 100 97 100 3722 3687 .651 1.535 1.589 1.8 1.59 1.39 104 288 1.33 .98 110 4340 5850 27 38 200 211 0 1924 242 1681 1.145 1930 1688 .873 1.185 .196 .245
14 3645 5043 460 336 3185 4707 3784 5159 473 354 3324 4823 0 0 856 991 161 136 100 100 99 100 7892 8147 .677 1.478 1.451 1.66 1.49 1.13 86 218 1.37 .99 100 4490 5850 28 38 216 226 0 3761 251 3511 1.102 3848 3597 .907 1.082 .14 .114
15 1504 2083 441 333 1063 1750 1505 2069 460 337 1064 1736 0 0 370 417 161 117 100 100 98 100 2813 2800 .607 1.646 1.632 1.85 1.59 .86 177 154 1.38 .98 150 4630 5850 25 40 227 242 0 1554 248 1305 1.228 1543 1295 .814 1.217 .296 .283
16 5330 8220 439 320 4891 7900 5212 8033 442 337 4773 7713 0 0 1507 1771 159 118 100 100 100 100 12791 12486 .619 1.615 1.616 1.69 1.64 .46 124 182 1.53 .99 120 4790 5860 28 40 245 257 0 6131 239 5892 1.205 5991 5753 .83 1.205 .269 .269
17 3052 3811 425 333 2627 3478 2958 3620 430 349 2533 3287 0 0 1037 841 144 120 100 100 100 100 6105 5820 .755 1.324 1.298 1.42 1.35 .44 79 245 1.23 .99 100 4930 5850 28 38 260 270 0 2842 248 2594 .987 2700 2452 1.013 .968 -.018 -.047
18 2453 3938 434 357 2019 3581 2578 4211 604 389 2144 3854 0 0 762 1201 2558 356 26 99 0 96 5600 5998 .564 1.774 1.798 1.84 1.75 .61 72 293 1.61 .99 90 5080 5840 27 36 275 284 0 2937 266 2671 1.323 3141 2874 .756 1.341 .404 .423
19 6348 9883 433 345 5915 9538 5968 9348 591 367 5535 9003 0 0 1627 2314 2470 250 100 100 75 100 15453 14538 .62 1.613 1.627 1.66 1.61 .37 79 314 1.54 .99 100 5220 5850 28 38 289 299 0 7371 257 7114 1.203 6972 6715 .831 1.213 .266 .279
20 2719 4236 434 339 2285 3897 2685 4265 456 353 2251 3926 0 0 497 717 236 137 100 100 100 100 6182 6177 .586 1.705 1.744 1.75 1.79 .4 37 362 1.56 .99 70 5370 5860 30 37 305 312 0 3159 253 2907 1.272 3181 2928 .786 1.301 .347 .379

Total number of rows: 41472

Table truncated, full table size 9618 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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