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Sample GSM741244 Query DataSets for GSM741244
Status Public on Nov 02, 2012
Title shfc20|CACO2
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 CACO2 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: CACO2
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/2006-06/68865.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 1774 2262 248 450 1526 1812 1754 2207 283 517 1506 1757 0 0 544 906 223 390 99 93 97 88 3338 3263 .842 1.187 1.167 1.31 1.18 .72 69 360 1.28 .98 90 2790 4860 65 74 74 83 0 2100 418 1682 1.102 2049 1631 .907 1.083 .141 .115
2 2036 2261 255 446 1781 1815 1998 2105 284 543 1743 1659 0 0 612 984 156 441 100 93 100 85 3596 3402 .981 1.019 .952 1.07 .93 .57 60 338 1.13 .97 80 2940 4850 65 73 90 98 0 2099 414 1685 .946 1954 1540 1.057 .884 -.08 -.178
3 3203 3879 268 467 2935 3412 3363 3843 287 553 3095 3376 0 0 780 1283 139 404 100 98 100 98 6347 6471 .86 1.163 1.091 1.19 1.14 .49 60 334 1.22 .99 80 3090 4850 65 73 105 113 0 3601 434 3168 1.079 3568 3134 .926 1.013 .11 .018
4 1491 3703 261 443 1230 3260 1437 3606 288 511 1176 3163 0 0 502 1429 143 375 100 100 100 98 4490 4339 .377 2.65 2.69 3.02 2.44 1.91 44 313 2.42 .97 70 3230 4860 66 73 119 126 0 3438 411 3027 2.461 3348 2937 .406 2.497 1.299 1.32
5 1214 1514 259 430 955 1084 1265 1520 277 496 1006 1090 0 0 433 742 145 406 100 83 93 65 2039 2096 .881 1.135 1.083 1.63 1.23 1.67 60 321 1.27 .96 80 3370 4860 66 74 133 141 0 1406 399 1006 1.054 1411 1012 .949 1.006 .076 .009
6 3132 3931 255 427 2877 3504 3230 3765 279 538 2975 3338 0 0 696 1393 147 442 100 100 100 100 6381 6313 .821 1.218 1.122 1.23 1.28 .45 44 391 1.26 .98 70 3520 4850 65 72 148 155 0 3650 396 3253 1.131 3496 3099 .884 1.042 .177 .059
7 1205 1448 234 393 971 1055 1165 1295 261 477 931 902 0 0 425 778 142 366 97 75 97 64 2026 1833 .92 1.087 .969 1.72 1.2 2.9 36 362 1.28 .94 70 3680 4860 66 73 164 171 0 1344 365 980 1.009 1202 837 .991 .9 .013 -.153
8 2763 3699 242 378 2521 3321 2730 3561 263 463 2488 3183 0 0 731 1402 132 364 100 100 100 97 5842 5671 .759 1.317 1.279 1.33 1.25 .5 60 308 1.35 .98 80 3810 4860 66 74 177 185 0 3434 351 3083 1.223 3306 2955 .818 1.188 .291 .248
9 1771 2244 250 437 1521 1807 1760 2090 260 501 1510 1653 0 0 422 845 134 365 100 98 100 92 3328 3163 .842 1.188 1.095 1.28 1.2 .7 86 278 1.26 .97 100 3960 4850 64 74 191 201 0 2083 406 1678 1.103 1940 1535 .907 1.016 .141 .023
10 3046 4186 249 465 2797 3721 3091 4148 264 535 2842 3683 0 0 678 1305 127 416 100 99 100 99 6518 6525 .752 1.33 1.296 1.38 1.32 .54 86 233 1.38 .99 100 4110 4860 65 75 206 216 0 3886 432 3455 1.235 3851 3419 .81 1.203 .305 .267
11 1489 1595 250 466 1239 1129 1504 1493 271 539 1254 1027 0 0 362 618 146 422 100 92 99 65 2368 2281 1.097 .911 .819 .97 .93 .58 86 226 1.09 .96 100 4250 4860 65 75 220 230 0 1481 433 1048 .846 1386 954 1.182 .76 -.241 -.395
12 2024 3590 264 444 1760 3146 2120 3493 292 541 1856 3049 0 0 514 1437 151 376 99 100 99 98 4906 4905 .559 1.788 1.643 1.92 1.79 1.08 80 244 1.81 .97 100 4400 4860 65 75 235 245 0 3333 412 2921 1.66 3243 2831 .603 1.525 .731 .609
13 2263 3163 260 432 2003 2731 2227 3128 274 520 1967 2696 0 0 578 1142 136 360 100 99 99 97 4734 4663 .733 1.363 1.371 1.48 1.43 .81 70 269 1.41 .97 90 4540 4860 65 74 249 258 0 2937 401 2536 1.266 2904 2503 .79 1.273 .34 .348
14 2969 4274 263 459 2706 3815 2931 4152 284 555 2668 3693 0 0 611 1361 224 558 100 100 100 99 6521 6361 .709 1.41 1.384 1.43 1.45 .5 97 265 1.45 .99 110 4690 4860 64 75 263 274 0 3968 426 3542 1.309 3855 3429 .764 1.285 .388 .362
15 1441 1818 253 461 1188 1357 1427 1774 272 526 1174 1313 0 0 398 730 130 337 100 91 100 84 2545 2487 .875 1.142 1.118 1.27 1.08 .98 80 251 1.27 .97 100 4840 4860 65 75 279 289 0 1688 428 1260 1.061 1647 1219 .943 1.038 .085 .054
16 8762 11045 245 431 8517 10614 8904 11366 268 518 8659 10935 0 0 1200 2044 127 403 100 100 100 100 19131 19594 .802 1.246 1.263 1.25 1.28 .26 70 272 1.27 .99 90 4990 4850 64 73 294 303 0 10255 400 9854 1.157 10553 10153 .864 1.172 .21 .23
17 2589 4125 280 438 2309 3687 2559 4081 296 491 2279 3643 0 0 555 1013 139 345 100 100 100 100 5996 5922 .626 1.597 1.599 1.65 1.64 .5 70 267 1.6 .99 90 5130 4850 64 73 308 317 0 3830 407 3423 1.483 3789 3382 .675 1.484 .568 .57
18 3424 5615 304 411 3120 5204 3376 5352 321 486 3072 4941 0 0 636 1498 142 344 100 100 100 100 8324 8013 .6 1.668 1.608 1.7 1.72 .52 80 235 1.65 .99 100 5280 4860 65 75 323 333 0 5213 382 4832 1.549 4969 4587 .646 1.493 .631 .579
19 8430 11179 298 420 8132 10759 8521 11022 318 483 8223 10602 0 0 1749 2632 131 345 100 100 100 100 18891 18825 .756 1.323 1.289 1.36 1.33 .38 104 212 1.33 .99 110 5420 4870 65 76 336 347 0 10379 390 9989 1.228 10233 9843 .814 1.197 .297 .259
20 4153 4471 280 416 3873 4055 4123 4351 297 487 3843 3935 0 0 788 1520 129 346 100 100 100 100 7928 7778 .955 1.047 1.024 1.05 1 .38 80 257 1.08 .97 100 5570 4860 65 75 352 362 0 4151 386 3765 .972 4040 3653 1.029 .951 -.041 -.073

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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