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Sample GSM741258 Query DataSets for GSM741258
Status Public on Nov 02, 2012
Title shfc39|SW480
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 SW480 genomic DNA
Organism Homo sapiens
Characteristics cell type: colorectal cancer
cell line: SW480
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/2006-06/68862.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
1 619 798 111 122 508 676 602 789 116 126 491 667 0 0 116 177 32 40 100 100 100 100 1184 1158 .751 1.331 1.358 1.35 1.32 .33 70 328 1.28 .99 90 2370 6530 84 93 64 73 0 899 137 762 1.499 889 752 .667 1.531 .584 .614
2 657 778 108 130 549 648 664 805 111 132 556 675 0 0 173 240 29 42 100 99 100 99 1197 1231 .847 1.18 1.214 1.21 1.18 .42 69 298 1.19 .99 90 2510 6520 83 92 78 87 0 877 146 730 1.33 907 761 .752 1.368 .411 .452
3 1177 1341 111 127 1066 1214 1240 1417 113 130 1129 1290 0 0 368 400 31 36 100 100 99 100 2280 2419 .878 1.139 1.143 1.29 1.16 .78 69 312 1.14 .99 90 2650 6520 83 92 92 101 0 1511 143 1368 1.283 1597 1454 .779 1.287 .36 .365
4 532 831 116 131 416 700 504 813 121 135 388 682 0 0 167 229 51 39 100 100 100 100 1116 1070 .594 1.683 1.758 1.83 1.75 .71 51 344 1.55 .98 80 2800 6520 84 92 108 116 0 936 148 789 1.896 916 768 .527 1.981 .923 .986
5 462 559 120 142 342 417 481 566 137 144 361 424 0 0 129 149 181 46 84 97 48 97 759 785 .82 1.219 1.175 1.37 1.25 .79 69 314 1.21 .98 90 2950 6520 83 92 122 131 0 630 160 470 1.374 638 478 .728 1.323 .458 .404
6 927 1091 123 138 804 953 975 1165 139 141 852 1027 0 0 246 366 177 47 100 100 95 100 1757 1879 .844 1.185 1.205 1.18 1.16 .46 60 331 1.19 .99 80 3090 6520 84 92 137 145 0 1229 155 1074 1.336 1313 1157 .749 1.358 .417 .442
7 380 474 123 136 257 338 365 475 126 139 242 339 0 0 91 125 32 41 100 100 100 98 595 581 .76 1.315 1.401 1.39 1.33 .58 44 330 1.25 .97 70 3240 6520 84 91 152 159 0 534 153 381 1.482 535 382 .675 1.578 .567 .658
8 892 1613 126 141 766 1472 947 1694 130 143 821 1553 0 0 199 368 34 38 100 100 100 100 2238 2374 .52 1.922 1.892 2.02 1.92 .77 64 245 1.8 .99 90 3380 6520 83 92 165 174 0 1817 159 1659 2.165 1909 1750 .462 2.131 1.115 1.092
9 600 740 129 138 471 602 629 757 134 142 500 619 0 0 147 158 31 38 100 100 98 100 1073 1119 .782 1.278 1.238 1.53 1.3 1.33 112 208 1.22 .99 120 3520 6520 82 94 178 190 0 834 155 678 1.44 853 697 .694 1.395 .526 .48
10 1092 1168 128 145 964 1023 1109 1191 131 147 981 1046 0 0 184 226 30 39 100 100 100 100 1987 2027 .942 1.061 1.066 1.08 1.08 .31 97 245 1.07 .99 110 3670 6510 81 92 193 204 0 1316 163 1153 1.196 1342 1179 .836 1.201 .258 .265
11 465 436 128 137 337 299 459 429 132 136 331 292 0 0 77 102 33 38 100 99 100 97 636 623 1.127 .887 .882 .9 .89 .34 97 250 .96 .98 110 3820 6510 81 92 208 219 0 491 154 337 1 483 329 1 .994 0 -.009
12 663 1014 131 139 532 875 675 1016 132 141 544 877 0 0 149 185 32 37 100 100 99 100 1407 1421 .608 1.645 1.612 1.8 1.61 .82 86 246 1.51 .99 100 3960 6520 83 93 223 233 0 1143 157 986 1.853 1145 988 .54 1.816 .89 .861
13 618 811 129 139 489 672 625 801 132 142 496 662 0 0 134 183 41 40 100 100 100 100 1161 1158 .728 1.374 1.335 1.45 1.33 .53 86 246 1.31 .99 100 4110 6520 83 93 238 248 0 914 157 757 1.548 903 746 .646 1.504 .631 .589
14 736 756 124 137 612 619 744 760 127 140 620 623 0 0 136 141 39 41 100 100 100 100 1231 1243 .989 1.011 1.005 1.04 1.06 .3 97 262 1.04 .99 110 4250 6510 81 92 251 262 0 852 154 697 1.14 856 702 .877 1.132 .189 .179
15 393 391 124 137 269 254 397 389 126 142 273 252 0 0 86 93 28 43 100 100 98 96 523 525 1.059 .944 .923 1.04 .93 .62 97 266 1 .98 110 4400 6510 81 92 266 277 0 441 154 286 1.064 438 284 .94 1.04 .089 .057
16 2651 3093 129 137 2522 2956 2658 3262 130 141 2529 3125 0 0 396 672 30 42 100 100 100 100 5478 5654 .853 1.172 1.236 1.16 1.18 .22 80 258 1.18 .99 100 4550 6510 82 92 282 292 0 3485 154 3331 1.321 3676 3521 .757 1.392 .401 .477
17 754 949 126 135 628 814 755 965 125 138 629 830 0 0 135 172 30 40 100 100 100 100 1442 1459 .771 1.296 1.32 1.33 1.33 .4 80 247 1.26 .99 100 4690 6510 82 92 296 306 0 1069 152 917 1.46 1087 935 .685 1.487 .546 .572
18 894 1008 123 134 771 874 936 1024 125 139 813 890 0 0 184 149 34 41 100 100 99 100 1645 1703 .882 1.134 1.095 1.28 1.1 .95 97 250 1.12 .99 110 4830 6510 81 92 309 320 0 1136 151 985 1.277 1154 1003 .783 1.233 .353 .303
19 1986 2404 121 132 1865 2272 1937 2325 128 135 1816 2193 0 0 468 535 53 44 100 100 100 100 4137 4009 .821 1.218 1.208 1.25 1.2 .32 97 253 1.21 .99 110 4970 6510 81 92 323 334 0 2709 149 2560 1.373 2620 2471 .729 1.361 .457 .444
20 665 696 122 134 543 562 686 718 128 137 564 584 0 0 164 164 54 46 100 99 100 99 1105 1148 .966 1.035 1.035 1.12 1.02 .58 112 228 1.05 .98 120 5130 6510 81 93 339 351 0 784 151 633 1.166 809 658 .857 1.167 .222 .222

Total number of rows: 41472

Table truncated, full table size 8989 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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