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Sample GSM350528 Query DataSets for GSM350528
Status Public on Jul 10, 2009
Title Shfc139|HCC1806
Sample type genomic
 
Channel 1
Source name Normal human female genomic DNA
Organism Homo sapiens
Characteristics Normal human female genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name Breast Tumor Cell Line HCC1806 genomic DNA
Organism Homo sapiens
Characteristics Breast Tumor Cell Line HCC1806 genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2000, 5240; Software: type: feature extraction; Performer: Melanie,,Bocanegra
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-07-30; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 550; Parameter Laser on time = 41724; Parameter Laser Power = 3.52; Parameter Scan Time = 10:17:03; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.68; Performer: Melanie,,Bocanegra
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2004-07-30; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 550; Parameter Scan Power = 100; Parameter Laser on time = 41768; Parameter Laser Power = 3.47; Parameter Scan Time = 10:17:03; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 28.68; Performer: Melanie,,Bocanegra
Description Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-09/55438.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 Dec 11, 2008
Last update date Jul 10, 2009
Contact name Jonathan Pollack
E-mail(s) pollack1@stanford.edu
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL7784
Series (2)
GSE13914 Molecular profiling of breast cancer cell lines defines relevant tumor models (aCGH)
GSE15376 Molecular profiling of breast cancer cell lines defines relevant tumor models

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 3795 3272 338 815 3457 2457 3925 3358 361 860 3587 2543 0 0 1262 1315 211 357 100 98 98 86 5914 6130 1.407 .711 .709 .69 .7 .28 58 357 .87 .98 80 2500 5640 36 44 46 54 0 2834 706 2128 .616 2909 2203 1.624 .614 -.7 -.703
2 2736 2048 335 847 2401 1201 2763 1985 358 870 2428 1138 0 0 744 706 200 300 100 89 100 78 3602 3566 1.999 .5 .469 .49 .5 .23 64 308 .78 .98 90 2650 5650 36 45 60 69 0 1774 734 1040 .433 1720 986 2.308 .406 -1.207 -1.3
3 3096 3427 335 811 2761 2616 2939 3332 350 842 2604 2521 0 0 893 959 145 296 100 100 100 100 5377 5125 1.055 .947 .968 .99 .97 .36 60 320 1.12 .98 80 2790 5650 37 45 75 83 0 2969 703 2266 .821 2886 2184 1.218 .839 -.285 -.254
4 1704 1983 321 757 1383 1226 1741 2048 336 807 1420 1291 0 0 401 615 141 302 100 94 98 80 2609 2711 1.128 .886 .909 .9 .83 .45 51 358 1.2 .98 80 2930 5640 36 44 89 97 0 1718 656 1062 .768 1774 1118 1.302 .788 -.381 -.345
5 1171 1098 321 819 850 279 1172 1061 347 850 851 242 0 0 337 320 154 306 98 44 95 16 1129 1093 3.047 .328 .284 .55 .35 .57 64 321 .96 .85 90 3080 5650 36 45 103 112 0 951 709 242 .284 919 210 3.517 .246 -1.814 -2.021
6 3187 3798 333 840 2854 2958 3103 3696 339 850 2770 2856 0 0 728 1015 142 287 100 100 100 100 5812 5626 .965 1.036 1.031 1.04 1.04 .31 44 362 1.2 .99 70 3230 5640 36 43 119 126 0 3290 728 2562 .898 3202 2474 1.114 .893 -.155 -.163
7 1147 892 334 852 813 40 1126 938 338 890 792 86 0 0 356 252 132 319 96 14 92 0 853 878 20.325 .049 .109 .52 .22 1.02 51 351 .83 .37 80 3370 5640 36 44 133 141 0 773 738 35 .043 813 74 23.463 .094 -4.552 -3.41
8 2790 3055 307 873 2483 2182 2755 3067 326 903 2448 2194 0 0 707 765 127 318 100 100 100 98 4665 4642 1.138 .879 .896 .9 .88 .31 60 313 1.11 .99 80 3510 5640 36 44 147 155 0 2646 756 1890 .761 2657 1901 1.314 .776 -.394 -.365
9 1900 1973 306 886 1594 1087 1898 1995 323 904 1592 1109 0 0 441 514 127 320 100 91 100 80 2681 2701 1.466 .682 .697 .71 .67 .38 97 269 1.07 .97 110 3660 5640 34 45 160 171 0 1709 768 942 .591 1728 961 1.693 .603 -.759 -.729
10 3226 4118 308 814 2918 3304 3256 4032 328 854 2948 3218 0 0 666 1011 132 327 100 100 100 100 6222 6166 .883 1.132 1.092 1.15 1.05 .36 96 230 1.28 .99 110 3810 5640 34 45 175 186 0 3567 705 2862 .981 3493 2788 1.02 .946 -.028 -.081
11 1702 2155 333 814 1369 1341 1707 2074 352 841 1374 1260 0 0 410 657 142 300 100 96 100 89 2710 2634 1.021 .98 .917 .99 .99 .45 97 253 1.3 .98 110 3950 5640 34 45 189 200 0 1867 705 1162 .849 1797 1091 1.178 .794 -.237 -.332
12 2257 2947 343 813 1914 2134 2220 3011 358 856 1877 2198 0 0 469 637 143 307 100 100 99 100 4048 4075 .897 1.115 1.171 1.18 1.1 .56 86 284 1.31 .99 100 4100 5640 35 45 205 215 0 2553 704 1849 .966 2608 1904 1.035 1.014 -.05 .021
13 2971 6195 339 822 2632 5373 3129 6380 355 850 2790 5558 0 0 715 1381 131 304 100 100 100 100 8005 8348 .49 2.041 1.992 2.14 2 .68 80 273 2.1 .99 100 4250 5640 35 45 220 230 0 5366 712 4654 1.768 5527 4815 .565 1.726 .822 .787
14 3440 5059 328 787 3112 4272 3514 5155 351 814 3186 4368 0 0 889 1458 139 274 100 100 100 100 7384 7554 .728 1.373 1.371 1.41 1.39 .46 97 263 1.48 .99 110 4390 5640 34 45 233 244 0 4382 682 3701 1.189 4466 3784 .841 1.188 .25 .248
15 1734 2486 337 779 1397 1707 1708 2336 349 804 1371 1557 0 0 306 672 133 264 100 100 100 100 3104 2928 .818 1.222 1.136 1.23 1.2 .47 80 263 1.44 .97 100 4540 5640 35 45 249 259 0 2154 675 1479 1.058 2024 1349 .945 .984 .082 -.024
16 10080 15083 320 797 9760 14286 9920 15799 344 822 9600 15002 0 0 1506 2847 139 292 100 100 100 100 24046 24602 .683 1.464 1.563 1.46 1.49 .24 80 274 1.51 1 100 4690 5640 35 45 264 274 0 13066 690 12375 1.268 13686 12996 .789 1.354 .343 .437
17 3029 4541 311 815 2718 3726 3023 4456 336 849 2712 3641 0 0 593 920 143 277 100 100 100 100 6444 6353 .729 1.371 1.343 1.39 1.43 .33 80 251 1.51 .99 100 4830 5640 35 45 278 288 0 3934 706 3228 1.188 3860 3154 .842 1.163 .248 .218
18 3440 4976 336 807 3104 4169 3572 5274 357 826 3236 4467 0 0 752 1178 148 286 99 100 99 99 7273 7703 .745 1.343 1.38 1.38 1.35 .45 97 255 1.46 .99 110 4970 5640 34 45 291 302 0 4310 699 3611 1.163 4569 3870 .859 1.196 .218 .258
19 5701 7218 362 794 5339 6424 5594 7338 378 821 5232 6544 0 0 1740 1927 143 282 100 100 100 100 11763 11776 .831 1.203 1.251 1.24 1.23 .32 104 247 1.29 .99 110 5120 5640 34 45 306 317 0 6253 688 5565 1.042 6357 5669 .959 1.083 .06 .116
20 1773 2043 362 829 1411 1214 1732 1985 374 846 1370 1156 0 0 397 468 144 308 100 98 100 94 2625 2526 1.162 .86 .844 .91 .87 .4 97 257 1.17 .98 110 5270 5640 34 45 321 332 0 1770 718 1052 .745 1720 1001 1.342 .731 -.424 -.452

Total number of rows: 41472

Table truncated, full table size 9507 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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