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Sample GSM741265 Query DataSets for GSM741265
Status Public on Nov 02, 2012
Title shfc40|SW837
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 SW837 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: SW837
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol model: GenePix 4000A
Description Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68863.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
1 497 665 119 125 378 540 516 682 123 128 397 557 0 0 142 160 34 39 100 100 96 100 918 954 .7 1.429 1.403 1.77 1.49 1.45 70 316 1.32 .98 90 2180 6710 86 95 77 86 0 633 119 514 1.36 649 530 .735 1.335 .443 .417
2 629 667 121 129 508 538 647 650 125 131 526 521 0 0 149 184 34 42 100 100 100 100 1046 1047 .944 1.059 .99 1.09 1.04 .38 64 266 1.07 .98 90 2330 6710 86 95 92 101 0 635 123 512 1.008 619 496 .992 .943 .012 -.085
3 832 1048 124 135 708 913 887 1108 126 138 763 973 0 0 264 369 31 41 99 100 99 99 1621 1736 .775 1.29 1.275 1.48 1.33 1.08 69 299 1.27 .98 90 2470 6700 85 94 106 115 0 998 129 869 1.227 1055 926 .815 1.214 .296 .28
4 507 902 120 132 387 770 504 906 120 133 384 774 0 0 109 142 30 40 100 100 100 100 1157 1158 .503 1.99 2.016 2.1 2 .64 44 307 1.75 .98 70 2620 6700 86 93 122 129 0 859 126 733 1.894 862 737 .528 1.919 .921 .94
5 422 364 118 123 304 241 429 372 120 128 311 249 0 0 98 92 32 40 98 98 95 94 545 560 1.261 .793 .801 .85 .83 .44 64 289 .88 .98 90 2760 6700 85 94 135 144 0 346 117 229 .755 354 237 1.325 .762 -.406 -.392
6 849 814 122 129 727 685 892 845 123 134 770 716 0 0 243 257 32 41 98 100 98 98 1412 1486 1.061 .942 .93 1.12 .94 1.36 60 321 .96 .99 80 2900 6700 86 94 150 158 0 775 123 652 .897 804 682 1.115 .885 -.157 -.176
7 399 421 123 129 276 292 393 405 122 132 270 276 0 0 111 107 30 41 100 100 100 100 568 546 .945 1.058 1.022 1.15 1.14 .43 44 349 1.04 .98 70 3050 6700 86 93 165 172 0 401 123 278 1.007 386 263 .993 .973 .01 -.039
8 786 661 119 134 667 527 781 667 122 137 662 533 0 0 132 114 31 44 100 100 100 100 1194 1195 1.266 .79 .805 .82 .79 .28 64 290 .85 .98 90 3200 6700 85 94 179 188 0 629 128 502 .752 635 507 1.33 .766 -.411 -.384
9 1363 1690 119 134 1244 1556 1402 1673 122 139 1283 1539 0 0 353 447 34 43 100 100 100 100 2800 2822 .799 1.251 1.2 1.36 1.23 .87 96 238 1.23 .99 110 3340 6710 85 96 192 203 0 1609 128 1481 1.191 1592 1465 .84 1.142 .252 .191
10 1562 2468 119 134 1443 2334 1603 2584 123 135 1484 2450 0 0 417 700 38 40 100 100 99 100 3777 3934 .618 1.617 1.651 1.7 1.56 .67 96 199 1.57 .99 110 3490 6720 86 97 207 218 0 2349 128 2222 1.54 2460 2332 .65 1.571 .623 .652
11 635 706 122 137 513 569 624 732 151 169 502 595 0 0 144 185 121 140 100 99 98 94 1082 1097 .902 1.109 1.185 1.15 1.18 .38 86 257 1.11 .98 100 3630 6700 85 95 222 232 0 672 130 542 1.056 697 566 .947 1.128 .078 .174
12 630 861 119 134 511 727 612 840 151 172 493 706 0 0 89 129 122 141 100 100 100 100 1238 1199 .703 1.423 1.432 1.44 1.43 .31 69 259 1.38 .99 90 3780 6710 86 95 237 246 0 820 128 692 1.354 800 672 .738 1.363 .437 .447
13 639 647 115 126 524 521 643 642 125 135 528 516 0 0 142 154 62 49 100 100 100 100 1045 1044 1.006 .994 .977 1.04 1.02 .41 79 274 1.02 .99 100 3920 6690 84 94 251 261 0 616 120 496 .946 611 491 1.057 .93 -.079 -.104
14 757 705 118 130 639 575 794 731 127 149 676 601 0 0 175 178 73 79 100 99 98 97 1214 1277 1.111 .9 .889 .98 .9 .57 112 230 .94 .99 120 4070 6700 84 96 265 277 0 671 124 547 .857 696 572 1.167 .846 -.223 -.241
15 1809 2394 117 136 1692 2258 1782 2522 126 149 1665 2386 0 0 516 652 53 77 100 100 100 100 3950 4051 .749 1.335 1.433 1.39 1.37 .47 69 237 1.33 1 90 4220 6710 86 95 281 290 0 2279 129 2149 1.27 2401 2271 .787 1.364 .345 .448
16 2563 3343 109 135 2454 3208 2730 3478 114 136 2621 3343 0 0 628 736 30 43 100 100 100 100 5662 5964 .765 1.307 1.275 1.44 1.28 .91 97 216 1.29 .99 110 4360 6700 84 95 294 305 0 3182 129 3054 1.244 3311 3182 .804 1.214 .315 .28
17 856 2006 111 132 745 1874 819 2039 115 137 708 1907 0 0 236 307 31 48 99 100 99 100 2619 2615 .398 2.515 2.694 2.64 2.7 .69 79 237 2.33 .99 100 4500 6690 84 94 309 319 0 1909 126 1784 2.394 1941 1815 .418 2.564 1.26 1.358
18 1483 2286 116 135 1367 2151 1498 2287 120 145 1382 2152 0 0 435 529 33 52 100 100 100 100 3518 3534 .636 1.574 1.557 1.64 1.61 .56 97 231 1.53 .99 110 4650 6700 84 95 323 334 0 2176 129 2047 1.498 2177 2048 .668 1.482 .583 .568
19 2305 3498 110 134 2195 3364 2307 3497 115 138 2197 3363 0 0 443 542 30 38 100 100 100 100 5559 5560 .652 1.533 1.531 1.59 1.54 .48 97 233 1.51 .99 110 4790 6690 83 94 337 348 0 3330 128 3202 1.459 3329 3201 .685 1.457 .545 .543
20 1116 1591 109 126 1007 1465 1138 1561 115 131 1029 1435 0 0 262 325 29 40 100 100 100 100 2472 2464 .687 1.455 1.395 1.53 1.45 .57 104 207 1.42 .99 110 4940 6700 84 95 352 363 0 1514 120 1394 1.385 1486 1366 .722 1.327 .47 .409

Total number of rows: 41472

Table truncated, full table size 9085 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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