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Sample GSM741246 Query DataSets for GSM741246
Status Public on Nov 02, 2012
Title shgu228|LIM1215
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 LIM1215 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: LIM1215
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/2006-08/69844.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 5162 3617 714 963 4448 2654 5105 3604 771 1040 4391 2641 0 0 1581 965 403 679 100 100 99 90 7102 7032 1.676 .597 .601 .63 .59 .33 97 310 .7 .99 110 2620 5840 26 37 28 39 0 2753 733 2020 .454 2743 2010 2.202 .458 -1.139 -1.127
2 6922 6593 729 1018 6193 5575 7266 6915 1225 1717 6537 5897 0 0 1940 1873 1530 2161 97 92 89 83 11768 12434 1.111 .9 .902 .94 .88 .41 64 316 .96 .99 90 2770 5850 28 37 44 53 0 5018 775 4244 .685 5264 4489 1.459 .687 -.545 -.542
3 8270 9275 690 937 7580 8338 8703 9550 731 992 8013 8613 0 0 1931 2399 289 413 100 99 99 98 15918 16626 .909 1.1 1.075 1.1 1.11 .24 97 262 1.13 .99 110 2910 5850 27 38 57 68 0 7060 713 6347 .837 7269 6556 1.194 .818 -.256 -.29
4 7204 6969 705 948 6499 6021 7256 7189 752 978 6551 6241 0 0 5883 3355 339 352 97 96 94 94 12520 12792 1.079 .926 .953 1.26 .97 2.25 72 294 .97 .97 90 3060 5850 28 37 73 82 0 5305 722 4583 .705 5472 4751 1.418 .725 -.504 -.464
5 7425 7142 735 965 6690 6177 7203 6977 769 987 6468 6012 0 0 1712 1379 311 355 100 100 100 100 12867 12480 1.083 .923 .929 .95 .93 .24 70 338 .96 .99 90 3200 5850 28 37 87 96 0 5436 735 4702 .703 5311 4576 1.423 .708 -.509 -.499
6 5933 5935 707 927 5226 5008 6228 5990 744 961 5521 5063 0 0 1826 1782 259 345 100 98 97 97 10234 10584 1.044 .958 .917 .99 .94 .35 58 315 .99 .99 80 3350 5850 29 37 103 111 0 4518 706 3812 .729 4559 3854 1.371 .698 -.455 -.519
7 6828 7433 668 862 6160 6571 6998 7463 705 916 6330 6601 0 0 1843 1905 266 361 100 100 100 99 12731 12931 .937 1.067 1.043 1.09 1.1 .31 146 222 1.09 .99 130 3500 5850 26 39 115 128 0 5658 656 5002 .812 5681 5025 1.232 .794 -.301 -.333
8 6117 6698 678 886 5439 5812 6011 6840 711 978 5333 5954 0 0 1062 1663 265 551 100 100 100 100 11251 11287 .936 1.069 1.116 1.07 1.06 .28 97 205 1.1 .99 110 3640 5850 27 38 130 141 0 5098 674 4424 .813 5206 4532 1.229 .85 -.298 -.235
9 5791 8173 684 903 5107 7270 5804 8057 715 949 5120 7154 0 0 1117 1361 273 466 100 100 100 100 12377 12274 .702 1.424 1.397 1.46 1.43 .36 86 223 1.42 .99 100 3790 5850 28 38 146 156 0 6221 687 5534 1.084 6133 5445 .923 1.064 .116 .089
10 8596 9306 684 942 7912 8364 8670 8980 731 970 7986 8038 0 0 2331 2205 332 340 100 100 99 100 16276 16024 .946 1.057 1.007 1.13 1.06 .41 72 261 1.08 .99 90 3930 5840 27 36 160 169 0 7084 717 6367 .805 6835 6118 1.243 .766 -.314 -.384
11 5038 6918 714 921 4324 5997 5067 6930 749 964 4353 6009 0 0 1044 1502 315 349 100 100 100 99 10321 10362 .721 1.387 1.38 1.42 1.47 .42 104 292 1.38 .99 110 4080 5840 26 37 174 185 0 5266 701 4565 1.056 5275 4574 .947 1.051 .078 .071
12 3590 4067 716 928 2874 3139 3628 4160 732 939 2912 3232 0 0 2337 2734 247 353 84 74 69 68 6013 6144 .916 1.092 1.11 1.25 1.14 1.01 80 269 1.13 .99 100 4230 5850 28 38 190 200 0 3096 706 2389 .831 3167 2460 1.203 .845 -.266 -.243
13 5252 7946 752 971 4500 6975 4981 7661 770 994 4229 6690 0 0 1646 1907 275 356 100 100 100 100 11475 10919 .645 1.55 1.582 1.63 1.61 .45 97 251 1.51 .99 110 4360 5850 27 38 202 213 0 6048 739 5309 1.18 5831 5092 .848 1.204 .239 .268
14 7311 7976 730 927 6581 7049 7495 8262 764 970 6765 7335 0 0 1611 1656 262 361 100 100 100 100 13630 14100 .934 1.071 1.084 1.09 1.09 .24 97 216 1.1 .99 110 4510 5850 27 38 217 228 0 6071 706 5366 .815 6289 5583 1.227 .825 -.295 -.277
15 3298 4746 688 877 2610 3869 3405 4737 721 906 2717 3860 0 0 798 1021 271 351 99 99 99 99 6479 6577 .675 1.482 1.421 1.65 1.49 1.06 192 169 1.43 .99 150 4650 5850 25 40 229 244 0 3613 668 2945 1.128 3606 2938 .886 1.081 .174 .113
16 9089 10581 715 887 8374 9694 8516 10105 745 926 7801 9218 0 0 2745 3256 261 341 100 100 100 100 18068 17019 .864 1.158 1.182 1.17 1.14 .26 104 245 1.17 .99 110 4810 5860 28 39 247 258 0 8054 675 7379 .881 7692 7017 1.135 .899 -.183 -.153
17 6899 10338 713 911 6186 9427 6777 10561 730 1075 6064 9650 0 0 1383 2217 259 1471 100 100 100 98 15613 15714 .656 1.524 1.591 1.53 1.59 .31 86 223 1.5 .99 100 4960 5850 28 38 263 273 0 7869 693 7176 1.16 8039 7345 .862 1.211 .214 .277
18 6304 11116 754 923 5550 10193 6492 11281 826 1092 5738 10358 0 0 2040 3276 840 1339 97 97 95 95 15743 16096 .544 1.837 1.805 1.97 1.85 .87 79 276 1.75 .99 100 5100 5840 27 37 277 287 0 8461 703 7759 1.398 8587 7884 .715 1.374 .483 .458
19 16524 27413 757 946 15767 26467 15948 27133 791 995 15191 26187 0 0 3089 4385 280 354 100 100 100 100 42234 41378 .596 1.679 1.724 1.7 1.67 .27 79 300 1.66 .99 100 5240 5850 28 38 291 301 0 20866 720 20146 1.278 20653 19933 .783 1.312 .354 .392
20 6469 10329 753 882 5716 9447 6539 10418 778 932 5786 9536 0 0 1071 1779 366 439 100 100 100 100 15163 15322 .605 1.653 1.648 1.68 1.67 .34 44 378 1.59 .99 70 5390 5860 30 37 307 314 0 7862 671 7191 1.258 7930 7259 .795 1.255 .331 .327

Total number of rows: 41472

Table truncated, full table size 9713 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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