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Sample GSM741264 Query DataSets for GSM741264
Status Public on Nov 02, 2012
Title shgu235|LS174T
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 LS174T genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: LS174T
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/2006-08/69655.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 4024 3520 547 799 3477 2721 4044 3440 584 821 3497 2641 0 0 714 786 303 426 100 99 100 99 6198 6138 1.278 .783 .755 .8 .75 .27 86 321 .88 .99 100 2670 5850 40 50 38 48 0 2470 561 1910 .549 2414 1853 1.821 .53 -.865 -.916
2 5265 5841 563 830 4702 5011 5441 5937 629 929 4878 5107 0 0 1387 1756 511 627 100 100 98 95 9713 9985 .938 1.066 1.047 1.1 1.1 .42 64 255 1.11 .98 90 2810 5860 41 50 52 61 0 4099 582 3517 .748 4166 3584 1.337 .735 -.419 -.445
3 6072 6408 543 795 5529 5613 6020 6328 577 841 5477 5533 0 0 1511 1609 213 381 100 100 100 100 11142 11010 .985 1.015 1.01 1.03 1 .26 97 287 1.06 .99 110 2950 5860 40 51 65 76 0 4497 558 3939 .712 4441 3883 1.404 .709 -.489 -.496
4 5049 4983 582 797 4467 4186 5393 4988 606 854 4811 4191 0 0 1280 1135 226 365 100 100 98 100 8653 9002 1.067 .937 .871 1.03 .96 .54 60 334 .99 .99 80 3100 5870 43 51 82 90 0 3497 559 2938 .658 3500 2941 1.521 .611 -.605 -.71
5 5323 4774 552 784 4771 3990 5216 4706 567 799 4664 3922 0 0 1376 1521 198 327 100 100 100 100 8761 8586 1.196 .836 .841 .83 .85 .24 80 323 .9 .99 100 3250 5860 41 51 96 106 0 3350 550 2800 .587 3303 2752 1.704 .59 -.769 -.761
6 4171 4669 545 781 3626 3888 4310 4841 566 809 3765 4060 0 0 1320 1249 204 330 98 100 98 100 7514 7825 .933 1.072 1.078 1.23 1.06 .77 51 343 1.12 .99 80 3390 5860 42 50 111 119 0 3277 548 2729 .752 3397 2849 1.329 .757 -.41 -.402
7 5193 5467 546 757 4647 4710 5011 5539 569 823 4465 4782 0 0 1306 1306 244 378 100 100 100 100 9357 9247 .987 1.014 1.071 1.04 1 .31 136 218 1.06 .99 130 3550 5860 39 52 124 137 0 3837 531 3305 .711 3887 3356 1.406 .752 -.491 -.412
8 4502 4371 545 746 3957 3625 4604 4367 567 812 4059 3621 0 0 1001 1294 243 386 100 100 100 100 7582 7680 1.092 .916 .892 .93 .91 .33 104 236 .98 .98 110 3680 5860 40 51 138 149 0 3067 524 2544 .643 3065 2541 1.555 .626 -.637 -.676
9 5948 5826 561 780 5387 5046 5873 5949 588 947 5312 5169 0 0 2184 1419 292 2082 100 97 100 78 10433 10481 1.068 .937 .973 .98 .97 .3 86 274 .98 .98 100 3840 5860 41 51 155 165 0 4089 547 3541 .657 4175 3628 1.521 .683 -.605 -.55
10 7070 6778 562 794 6508 5984 7074 6951 593 936 6512 6157 0 0 1723 1721 288 2076 100 94 100 93 12492 12669 1.088 .919 .945 .91 .97 .24 70 275 .96 .99 90 3980 5860 41 50 169 178 0 4757 557 4199 .645 4878 4321 1.55 .664 -.632 -.592
11 3622 4946 545 790 3077 4156 3577 4883 577 832 3032 4093 0 0 840 1052 245 402 100 100 100 100 7233 7125 .74 1.351 1.35 1.4 1.39 .38 97 345 1.38 .99 110 4120 5850 39 50 182 193 0 3471 554 2917 .948 3427 2872 1.055 .947 -.077 -.078
12 3614 4460 554 815 3060 3645 3772 4608 578 851 3218 3793 0 0 873 1330 218 368 100 100 100 100 6705 7011 .84 1.191 1.179 1.21 1.19 .42 44 331 1.25 .99 70 4270 5870 43 50 199 206 0 3130 572 2558 .836 3234 2662 1.196 .827 -.259 -.274
13 5121 7733 560 818 4561 6915 4994 7525 582 837 4434 6707 0 0 1365 1915 205 337 100 100 100 100 11476 11141 .66 1.516 1.513 1.57 1.54 .41 97 314 1.51 .99 110 4410 5860 40 51 211 222 0 5427 574 4853 1.064 5281 4707 .94 1.062 .089 .086
14 6031 6924 566 787 5465 6137 5939 6892 584 827 5373 6105 0 0 976 1199 193 345 100 100 100 100 11602 11478 .891 1.123 1.136 1.15 1.15 .32 86 260 1.16 .99 100 4560 5860 41 51 227 237 0 4859 552 4307 .788 4837 4284 1.269 .797 -.344 -.327
15 3176 4733 539 763 2637 3970 3088 4742 577 852 2549 3979 0 0 761 1101 214 691 99 99 99 99 6607 6528 .664 1.505 1.561 1.59 1.54 .55 177 189 1.49 .98 150 4700 5860 38 53 238 253 0 3322 535 2786 1.057 3328 2792 .946 1.095 .079 .132
16 14908 22683 579 811 14329 21872 15158 23515 598 861 14579 22704 0 0 2494 3858 250 692 100 100 100 100 36201 37283 .655 1.526 1.557 1.53 1.56 .24 124 183 1.53 .99 120 4860 5870 41 53 256 268 0 15919 569 15349 1.071 16502 15933 .934 1.093 .099 .128
17 6383 8349 563 801 5820 7548 6156 8008 585 810 5593 7207 0 0 1376 1806 224 335 100 100 100 100 13368 12800 .771 1.297 1.289 1.32 1.33 .29 86 241 1.31 .99 100 5000 5860 41 51 271 281 0 5859 562 5297 .91 5620 5058 1.099 .904 -.136 -.145
18 5746 8914 546 776 5200 8138 6003 9254 579 799 5457 8478 0 0 1720 1940 208 323 100 100 100 100 13338 13935 .639 1.565 1.554 1.74 1.69 .73 79 309 1.55 .99 100 5140 5850 40 50 285 295 0 6256 545 5711 1.098 6494 5950 .911 1.09 .135 .125
19 13408 20889 557 784 12851 20105 13835 21523 572 827 13278 20739 0 0 2393 3252 199 346 100 100 100 100 32956 34017 .639 1.564 1.562 1.59 1.54 .32 86 309 1.56 .99 100 5290 5860 41 51 300 310 0 14660 550 14109 1.098 15104 14554 .911 1.096 .135 .132
20 4730 6825 566 822 4164 6003 4684 7180 581 839 4118 6358 0 0 1420 1624 205 346 100 100 100 100 10167 10476 .694 1.442 1.544 1.56 1.45 .52 52 347 1.44 .99 80 5440 5870 43 51 316 324 0 4790 577 4213 1.012 5039 4462 .988 1.084 .017 .116

Total number of rows: 41472

Table truncated, full table size 9792 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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