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Sample GSM741271 Query DataSets for GSM741271
Status Public on Nov 02, 2012
Title shgu236|LS180
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 LS180 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: LS180
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/2006-08/69478.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 4212 2288 608 749 3604 1539 4322 2306 679 817 3714 1557 0 0 929 602 456 565 99 97 98 74 5143 5271 2.342 .427 .419 .45 .43 .22 86 310 .56 .98 100 2610 5850 32 42 32 42 0 2050 671 1379 .383 2066 1395 2.614 .376 -1.386 -1.413
2 4922 3284 632 759 4290 2525 5128 3382 652 768 4496 2623 0 0 1328 1043 253 244 100 97 100 95 6815 7119 1.699 .589 .583 .61 .6 .28 61 259 .68 .98 90 2750 5860 33 42 46 55 0 2942 680 2262 .527 3030 2350 1.896 .523 -.923 -.936
3 6282 4652 595 738 5687 3914 6204 4567 617 744 5609 3829 0 0 1160 1045 235 255 100 100 100 100 9601 9438 1.453 .688 .683 .69 .68 .17 86 268 .74 .99 100 2900 5860 33 43 61 71 0 4168 661 3507 .617 4092 3431 1.622 .612 -.697 -.709
4 4752 3333 612 729 4140 2604 5195 3539 633 741 4583 2810 0 0 1434 888 233 252 97 100 95 95 6744 7393 1.59 .629 .613 .7 .64 .41 58 338 .7 .99 80 3040 5870 35 43 76 84 0 2986 653 2333 .564 3171 2518 1.774 .549 -.827 -.864
5 4551 2506 621 696 3930 1810 4737 2508 637 723 4116 1812 0 0 892 605 236 257 100 100 100 99 5740 5928 2.171 .461 .44 .46 .47 .14 80 334 .56 .99 100 3190 5860 33 43 90 100 0 2245 624 1622 .413 2247 1624 2.423 .394 -1.277 -1.342
6 4845 2877 651 702 4194 2175 4992 3067 654 730 4341 2365 0 0 1045 742 218 253 100 100 100 97 6369 6706 1.928 .519 .545 .53 .55 .23 37 319 .6 .99 70 3340 5870 35 42 106 113 0 2578 629 1949 .465 2748 2119 2.152 .488 -1.106 -1.035
7 4640 2948 626 704 4014 2244 4798 2969 648 731 4172 2265 0 0 1059 744 227 254 100 99 100 99 6258 6437 1.789 .559 .543 .56 .56 .18 151 194 .64 .99 140 3490 5860 31 45 118 132 0 2641 631 2011 .501 2660 2029 1.996 .486 -.997 -1.04
8 4532 3486 612 734 3920 2752 4419 3506 657 741 3807 2772 0 0 888 564 242 254 100 100 100 100 6672 6579 1.424 .702 .728 .72 .72 .22 86 217 .77 .99 100 3630 5860 33 43 134 144 0 3123 658 2466 .629 3141 2484 1.59 .652 -.669 -.616
9 3560 3656 609 709 2951 2947 3581 3622 623 728 2972 2913 0 0 788 838 215 248 100 100 100 100 5898 5885 1.001 .999 .98 1.03 1 .35 86 263 1.03 .99 100 3780 5860 33 43 149 159 0 3276 635 2640 .895 3245 2610 1.118 .878 -.16 -.187
10 6046 5441 616 713 5430 4728 6273 5778 626 738 5657 5065 0 0 1966 1464 205 244 98 100 95 98 10158 10722 1.148 .871 .895 .94 .87 .39 60 265 .9 .99 80 3930 5860 34 42 165 173 0 4875 639 4236 .78 5177 4538 1.282 .802 -.358 -.318
11 2575 2732 594 752 1981 1980 2594 2752 624 776 2000 2000 0 0 723 565 241 262 100 100 99 100 3961 4000 1.001 .999 1 1.11 1.03 .5 97 322 1.06 .98 110 4060 5850 31 42 176 187 0 2448 674 1774 .896 2466 1792 1.117 .896 -.159 -.158
12 4045 3421 619 760 3426 2661 3930 3327 636 777 3311 2567 0 0 901 939 236 274 100 100 100 100 6087 5878 1.287 .777 .775 .79 .82 .24 37 325 .86 .99 70 4220 5870 35 42 194 201 0 3065 681 2384 .696 2981 2300 1.437 .695 -.523 -.526
13 3353 3830 584 716 2769 3114 3104 3768 597 734 2520 3052 0 0 1010 913 232 251 100 100 100 100 5883 5572 .889 1.125 1.211 1.2 1.14 .38 97 290 1.13 .99 110 4350 5860 32 43 205 216 0 3432 642 2790 1.008 3376 2735 .992 1.085 .011 .118
14 5664 4391 581 744 5083 3647 5533 4282 595 762 4952 3538 0 0 1091 724 219 238 100 100 100 100 8730 8490 1.394 .717 .714 .74 .71 .2 79 264 .77 .99 100 4500 5860 33 43 221 231 0 3934 667 3268 .643 3837 3170 1.556 .64 -.637 -.644
15 2497 2849 588 731 1909 2118 2479 2822 1147 825 1891 2091 0 0 707 585 4029 541 1 99 0 96 4027 3982 .901 1.109 1.106 1.24 1.11 .6 166 157 1.14 .98 140 4650 5860 31 45 234 248 0 2553 655 1898 .994 2528 1874 1.006 .991 -.009 -.013
16 8853 10719 611 757 8242 9962 8943 10929 1107 829 8332 10172 0 0 2404 2337 3886 520 96 100 61 100 18204 18504 .827 1.209 1.221 1.44 1.22 1.96 124 169 1.21 .99 120 4800 5870 33 45 250 262 0 9604 678 8926 1.083 9792 9114 .923 1.094 .115 .129
17 4562 4589 564 761 3998 3828 4381 4468 587 777 3817 3707 0 0 1389 1001 213 275 100 100 100 100 7826 7524 1.044 .957 .971 1.02 .99 .35 86 227 1.01 .99 100 4940 5860 33 43 265 275 0 4112 682 3430 .858 4003 3321 1.166 .87 -.221 -.201
18 4514 5382 569 728 3945 4654 4621 5566 579 756 4052 4838 0 0 1434 1341 207 263 97 99 96 99 8599 8890 .848 1.18 1.194 1.27 1.22 .39 70 302 1.21 .99 90 5090 5860 33 42 280 289 0 4822 652 4170 1.057 4987 4335 .946 1.07 .08 .097
19 10910 13063 587 732 10323 12331 10376 13026 590 744 9789 12294 0 0 2370 2625 222 241 100 100 100 100 22654 22083 .837 1.195 1.256 1.2 1.23 .19 79 302 1.2 .99 100 5230 5860 33 43 294 304 0 11704 656 11048 1.07 11671 11015 .934 1.125 .098 .17
20 4557 5604 561 738 3996 4866 4623 5486 587 770 4062 4748 0 0 864 933 236 264 100 100 100 100 8862 8810 .821 1.218 1.169 1.25 1.2 .3 37 353 1.23 .99 70 5380 5870 35 42 310 317 0 5021 661 4360 1.091 4915 4254 .917 1.047 .126 .067

Total number of rows: 41472

Table truncated, full table size 9680 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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