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Sample GSM741263 Query DataSets for GSM741263
Status Public on Nov 02, 2012
Title shfc78|SW403
Sample type genomic
 
Channel 1
Source name Normal human genomic DNA
Organism Homo sapiens
Characteristics reference: Normal human genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SW403 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: SW403
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/2006-07/69148.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 2402 2698 353 485 2049 2213 2612 2744 425 541 2259 2259 0 0 879 982 335 370 98 98 90 93 4262 4518 .926 1.08 1 1.24 1.11 .6 60 349 1.13 .98 80 2760 5420 82 90 72 80 0 2267 408 1860 .908 2306 1898 1.102 .84 -.14 -.251
2 2614 2527 288 522 2326 2005 2780 2517 310 576 2492 1995 0 0 767 1055 151 366 100 96 100 90 4331 4487 1.16 .862 .801 .92 .84 .52 52 331 .97 .96 80 2890 5420 82 90 85 93 0 2124 439 1685 .724 2115 1676 1.381 .673 -.465 -.572
3 5207 5542 305 530 4902 5012 5275 5482 323 605 4970 4952 0 0 1119 1183 162 410 100 100 100 100 9914 9922 .978 1.022 .996 1.05 1.03 .3 44 373 1.06 .99 70 3030 5420 82 89 99 106 0 4657 445 4212 .859 4607 4161 1.164 .837 -.219 -.256
4 2176 1866 297 552 1879 1314 2200 1969 322 598 1903 1417 0 0 519 671 156 379 100 91 100 75 3193 3320 1.43 .699 .745 .73 .76 .34 44 383 .88 .97 70 3180 5420 82 89 114 121 0 1568 464 1104 .588 1655 1191 1.702 .626 -.767 -.676
5 1778 1943 284 586 1494 1357 1651 1718 309 600 1367 1132 0 0 554 791 148 370 100 94 100 75 2851 2499 1.101 .908 .828 .97 .85 .61 52 355 1.12 .97 80 3330 5420 82 90 129 137 0 1633 492 1140 .763 1444 951 1.31 .696 -.39 -.523
6 4750 4853 293 589 4457 4264 4811 4632 326 632 4518 4043 0 0 1127 1376 166 386 100 100 100 100 8721 8561 1.045 .957 .895 .97 .96 .32 37 426 1.03 .99 70 3470 5410 81 88 143 150 0 4078 495 3583 .804 3892 3397 1.244 .752 -.315 -.411
7 1506 1977 294 575 1212 1402 1512 1968 331 639 1218 1393 0 0 507 724 166 374 97 94 94 85 2614 2611 .864 1.157 1.144 1.27 1.1 .65 34 406 1.31 .98 60 3620 5410 82 88 159 165 0 1661 483 1178 .972 1654 1171 1.029 .961 -.041 -.057
8 3738 6436 299 596 3439 5840 3868 6667 325 672 3569 6071 0 0 1054 2091 168 422 100 100 100 100 9279 9640 .589 1.698 1.701 1.75 1.64 .63 60 367 1.75 .99 80 3760 5410 81 89 172 180 0 5408 501 4908 1.427 5603 5102 .701 1.429 .513 .515
9 3046 3827 316 629 2730 3198 3090 3745 333 692 2774 3116 0 0 500 1451 164 463 100 98 100 95 5928 5890 .854 1.171 1.123 1.19 1.14 .62 60 364 1.28 .98 80 3910 5410 81 89 187 195 0 3216 529 2687 .984 3147 2619 1.016 .944 -.023 -.083
10 5375 7049 334 570 5041 6479 5292 7136 381 658 4958 6566 0 0 1255 2327 220 459 100 100 100 100 11520 11524 .778 1.285 1.324 1.27 1.25 .4 60 350 1.33 .99 80 4060 5410 81 89 202 210 0 5924 479 5445 1.08 5997 5518 .926 1.113 .111 .154
11 2619 2868 338 554 2281 2314 2565 2937 388 628 2227 2383 0 0 624 844 241 424 100 100 100 95 4595 4610 .986 1.014 1.07 1.06 .99 .46 60 364 1.12 .98 80 4200 5410 81 89 216 224 0 2410 466 1945 .852 2468 2003 1.173 .899 -.23 -.153
12 3246 4682 309 544 2937 4138 3251 4794 326 597 2942 4250 0 0 850 1440 169 397 100 98 100 97 7075 7192 .71 1.409 1.445 1.46 1.39 .61 60 371 1.46 .98 80 4350 5410 81 89 231 239 0 3934 457 3477 1.184 4029 3571 .845 1.214 .244 .28
13 5214 7658 348 579 4866 7079 5126 7611 392 647 4778 7032 0 0 1056 1802 224 404 100 100 100 100 11945 11810 .687 1.455 1.472 1.47 1.39 .4 44 370 1.48 .99 70 4480 5420 82 89 244 251 0 6435 487 5949 1.223 6396 5909 .818 1.237 .29 .307
14 5479 5683 403 609 5076 5074 5888 5974 462 686 5485 5365 0 0 1752 1734 254 417 98 100 97 100 10150 10850 1 1 .978 1.13 .97 .68 58 340 1.05 .99 80 4640 5440 84 92 260 268 0 4776 512 4264 .84 5020 4508 1.19 .822 -.252 -.283
15 2719 4607 368 586 2351 4021 2699 4471 411 631 2331 3885 0 0 726 1508 208 380 100 100 100 98 6372 6216 .585 1.71 1.667 1.82 1.75 .81 60 351 1.74 .97 80 4790 5410 81 89 275 283 0 3871 492 3379 1.437 3757 3265 .696 1.401 .523 .486
16 16614 21185 373 635 16241 20550 17395 21879 411 681 17022 21244 0 0 2872 3956 251 394 100 100 100 100 36791 38266 .79 1.265 1.248 1.27 1.32 .2 52 351 1.28 .99 80 4930 5420 82 90 289 297 0 17803 534 17269 1.063 18386 17852 .94 1.049 .089 .069
17 4994 7600 355 691 4639 6909 4915 7922 381 731 4560 7231 0 0 917 1941 179 401 100 100 100 100 11548 11791 .671 1.489 1.586 1.5 1.49 .41 51 368 1.55 .99 80 5070 5410 81 89 303 311 0 6387 581 5806 1.252 6657 6077 .799 1.333 .324 .414
18 6320 10221 332 654 5988 9567 6649 10404 354 728 6317 9750 0 0 1363 2368 163 459 100 100 100 100 15555 16067 .626 1.598 1.543 1.65 1.61 .47 60 343 1.64 .99 80 5220 5410 81 89 318 326 0 8589 550 8040 1.343 8743 8193 .745 1.297 .425 .375
19 12896 18840 328 638 12568 18202 13220 18999 355 724 12892 18361 0 0 2967 4264 192 455 100 100 100 100 30770 31253 .69 1.448 1.424 1.48 1.47 .33 69 367 1.46 .99 90 5360 5410 80 89 331 340 0 15832 536 15296 1.217 15966 15429 .822 1.197 .283 .259
20 4403 3936 306 620 4097 3316 4370 3898 331 691 4064 3278 0 0 710 1141 181 435 100 100 100 100 7413 7342 1.236 .809 .807 .81 .84 .29 60 357 .91 .98 80 5520 5410 81 89 348 356 0 3308 521 2787 .68 3276 2755 1.47 .678 -.556 -.561

Total number of rows: 41472

Table truncated, full table size 9799 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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