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Sample GSM741261 Query DataSets for GSM741261
Status Public on Nov 02, 2012
Title shfc109|HT29
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 HT29 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: HT29
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/2006-06/68861.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 1818 2431 367 688 1451 1743 1822 2254 391 795 1455 1566 0 0 437 1038 157 497 100 91 100 74 3194 3021 .832 1.201 1.076 1.33 1.14 .88 80 316 1.34 .95 100 2530 5310 58 68 60 70 0 2463 697 1766 1.217 2283 1586 .822 1.09 .283 .125
2 2154 2294 388 763 1766 1531 2174 2072 398 856 1786 1309 0 0 481 1009 152 521 100 86 99 62 3297 3095 1.153 .867 .733 .94 .74 .91 69 327 1.09 .95 90 2670 5300 57 66 74 83 0 2324 773 1551 .878 2099 1326 1.139 .742 -.187 -.43
3 3326 3418 383 689 2943 2729 3305 3257 391 780 2922 2568 0 0 795 1128 147 453 100 100 100 95 5672 5490 1.078 .927 .879 .95 .89 .38 60 351 1.03 .98 80 2820 5300 58 66 90 98 0 3462 698 2765 .939 3299 2601 1.065 .89 -.09 -.168
4 1798 2711 366 650 1432 2061 1770 2616 377 772 1404 1966 0 0 638 1189 142 477 100 94 100 83 3493 3370 .695 1.439 1.4 1.7 1.35 1.31 52 333 1.53 .97 80 2970 5310 59 67 105 113 0 2746 658 2088 1.458 2650 1992 .686 1.419 .544 .504
5 1352 1648 359 720 993 928 1315 1599 375 799 956 879 0 0 349 703 158 470 99 73 97 47 1921 1835 1.07 .935 .919 1.19 .93 1.04 70 331 1.25 .94 90 3110 5300 57 66 118 127 0 1669 729 940 .947 1620 890 1.056 .931 -.079 -.102
6 3328 2851 357 766 2971 2085 3322 2702 372 803 2965 1936 0 0 605 1086 157 479 100 94 100 87 5056 4901 1.425 .702 .653 .71 .74 .36 52 330 .89 .97 80 3260 5310 59 67 134 142 0 2888 776 2112 .711 2737 1961 1.407 .661 -.492 -.596
7 1042 1397 346 694 696 703 1042 1423 376 778 696 729 0 0 319 748 159 470 94 61 92 36 1399 1425 .99 1.01 1.047 1.33 1.15 1.1 36 360 1.35 .92 70 3400 5310 59 66 148 155 0 1415 703 712 1.023 1442 738 .977 1.061 .033 .085
8 2557 2937 332 690 2225 2247 2644 2774 355 758 2312 2084 0 0 779 1171 146 477 100 95 100 91 4472 4396 .99 1.01 .901 1.16 1.01 .71 44 366 1.15 .96 70 3550 5300 58 65 163 170 0 2975 699 2276 1.023 2810 2111 .977 .913 .033 -.131
9 1856 2276 333 722 1523 1554 1909 2188 362 764 1576 1466 0 0 337 904 149 448 100 90 100 77 3077 3042 .98 1.02 .93 1.06 1.09 .57 70 284 1.24 .97 90 3690 5310 58 67 176 185 0 2306 731 1574 1.034 2216 1485 .967 .942 .048 -.086
10 2951 3451 347 681 2604 2770 2898 3496 368 750 2551 2815 0 0 588 1089 156 453 100 100 100 97 5374 5366 .94 1.064 1.103 1.1 1.1 .47 97 258 1.17 .98 110 3840 5300 56 67 190 201 0 3496 690 2806 1.078 3541 2852 .928 1.118 .108 .161
11 1371 1256 335 730 1036 526 1366 1268 355 806 1031 538 0 0 367 611 151 484 100 53 98 24 1562 1569 1.97 .508 .522 .77 .64 .67 97 253 .95 .88 110 3980 5300 56 67 204 215 0 1272 739 533 .514 1284 545 1.944 .529 -.959 -.92
12 1793 2055 339 740 1454 1315 1742 1919 359 813 1403 1179 0 0 440 833 145 446 99 86 99 71 2769 2582 1.106 .904 .84 1.05 .88 .83 97 274 1.18 .94 110 4130 5300 56 67 219 230 0 2082 750 1332 .916 1944 1194 1.092 .851 -.126 -.232
13 2136 3079 347 776 1789 2303 2174 2892 353 843 1827 2116 0 0 526 1034 130 477 100 99 100 93 4092 3943 .777 1.287 1.158 1.42 1.23 .94 86 235 1.44 .98 100 4280 5310 58 68 235 245 0 3119 786 2333 1.304 2930 2144 .767 1.173 .383 .231
14 2625 2163 342 767 2283 1396 2658 2140 351 854 2316 1373 0 0 479 796 140 480 100 85 100 67 3679 3689 1.635 .611 .593 .66 .59 .45 97 250 .86 .96 110 4420 5300 56 67 248 259 0 2191 777 1414 .619 2168 1391 1.614 .601 -.691 -.736
15 1174 1237 347 768 827 469 1151 1145 363 848 804 377 0 0 306 638 138 467 100 46 98 22 1296 1181 1.763 .567 .469 .98 .68 .92 97 269 1.08 .83 110 4570 5300 56 67 263 274 0 1253 778 475 .574 1160 382 1.741 .475 -.8 -1.074
16 7920 10409 358 770 7562 9639 7970 10105 364 857 7612 9335 0 0 1013 2161 142 487 100 100 100 100 17201 16947 .785 1.275 1.226 1.28 1.3 .29 80 261 1.33 .99 100 4720 5310 58 68 279 289 0 10544 780 9764 1.291 10236 9456 .774 1.242 .369 .313
17 2929 4101 351 658 2578 3443 2915 4189 352 744 2564 3531 0 0 584 1379 140 453 100 99 100 99 6021 6095 .749 1.336 1.377 1.38 1.37 .61 86 258 1.42 .98 100 4870 5300 57 67 294 304 0 4154 667 3488 1.353 4243 3577 .739 1.395 .436 .48
18 3247 4042 357 692 2890 3350 3248 4075 356 755 2891 3383 0 0 438 1154 139 501 100 99 100 98 6240 6274 .863 1.159 1.17 1.18 1.16 .46 97 244 1.26 .99 110 5010 5300 56 67 307 318 0 4095 701 3394 1.174 4128 3427 .852 1.185 .232 .245
19 8142 9851 367 736 7775 9115 7966 9686 366 802 7599 8950 0 0 1516 2050 143 526 100 100 100 100 16890 16549 .853 1.172 1.178 1.18 1.19 .26 104 242 1.22 .99 110 5160 5300 56 67 322 333 0 9979 746 9234 1.188 9812 9066 .842 1.193 .248 .255
20 2219 2632 355 724 1864 1908 2170 2555 369 809 1815 1831 0 0 479 774 134 486 100 98 100 91 3772 3646 .977 1.024 1.009 1.06 .96 .47 104 260 1.21 .98 110 5310 5300 56 67 337 348 0 2666 733 1933 1.037 2588 1855 .964 1.022 .052 .031

Total number of rows: 41472

Table truncated, full table size 9619 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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