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Sample GSM350509 Query DataSets for GSM350509
Status Public on Jul 10, 2009
Title shei189_sr|H55785 vs. NF|
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 H55785 genomic DNA
Organism Homo sapiens
Characteristics Breast Tumor Cell Line H55785 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 = 1920, 8440; Software: type: feature extraction; Performer: Jessica,,Kao
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-11-13; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 600; Parameter Laser on time = 10272; Parameter Laser Power = 3.39; Parameter Scan Time = 16:04:45; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.39; Performer: Jessica,,Kao
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2003-11-13; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 680; Parameter Scan Power = 100; Parameter Laser on time = 10315; Parameter Laser Power = 3.53; Parameter Scan Time = 16:04:45; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 30.39; Performer: Jessica,,Kao
Description Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54197.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) [email protected]
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 GPL7782
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 1090 1088 275 577 815 511 1088 982 301 641 813 405 0 0 371 718 164 470 100 43 95 24 1326 1218 1.595 .627 .498 .93 .85 .71 37 443 1.03 .92 70 2060 8690 21 28 10 17 0 1167 619 548 .672 1053 434 1.487 .534 -.572 -.904
2 1170 835 273 556 897 279 1132 814 297 631 859 258 0 0 758 488 144 451 90 35 73 13 1176 1117 3.215 .311 .3 1.34 .53 2.2 52 342 .71 .73 80 2210 8710 23 31 25 33 0 896 596 299 .334 873 277 2.998 .322 -1.584 -1.634
3 1113 1424 268 588 845 836 1029 1302 295 665 761 714 0 0 460 636 153 445 97 76 97 38 1681 1475 1.011 .989 .938 1.16 .89 .82 37 417 1.33 .96 70 2350 8690 21 28 39 46 0 1527 631 897 1.061 1396 766 .942 1.006 .086 .009
4 1204 686 271 568 933 118 1251 634 296 634 980 66 0 0 509 444 156 430 92 19 81 5 1051 1046 7.907 .126 .067 .43 .31 .45 37 362 .62 .76 70 2500 8700 22 29 54 61 0 736 609 127 .136 680 71 7.372 .072 -2.882 -3.791
5 1401 1230 271 512 1130 718 1407 1017 286 568 1136 505 0 0 610 729 136 390 96 56 94 46 1848 1641 1.574 .635 .445 .82 .57 .63 52 397 .9 .91 80 2640 8690 21 29 68 76 0 1319 549 770 .682 1091 542 1.467 .477 -.553 -1.069
6 1298 933 267 505 1031 428 1314 842 287 565 1047 337 0 0 509 571 143 399 91 47 88 25 1459 1384 2.409 .415 .322 .63 .56 .51 32 416 .75 .89 60 2790 8690 22 28 84 90 0 1001 542 459 .445 903 361 2.246 .345 -1.167 -1.534
7 1146 1220 283 499 863 721 1084 1054 300 560 801 555 0 0 531 709 159 392 94 63 87 42 1584 1356 1.197 .835 .693 1.7 .93 4.85 52 361 1.1 .94 80 2930 8690 21 29 97 105 0 1309 535 773 .896 1130 595 1.116 .743 -.158 -.428
8 839 937 269 472 570 465 841 759 286 567 572 287 0 0 421 668 145 406 77 42 68 29 1035 859 1.226 .816 .502 1.5 1.01 1.62 69 340 1.14 .9 90 3070 8680 19 28 110 119 0 1005 506 499 .875 814 308 1.143 .538 -.193 -.894
9 569 739 264 438 305 301 430 694 292 540 166 256 0 0 365 503 149 409 51 44 41 14 606 422 1.013 .987 1.542 4.17 1.59 7.24 80 325 1.3 .75 100 3210 8670 18 28 124 134 0 793 470 323 1.058 744 275 .945 1.654 .082 .726
10 1477 1155 252 495 1225 660 1568 1043 280 564 1316 548 0 0 422 734 145 394 100 58 98 35 1885 1864 1.856 .539 .416 .65 .55 .51 52 367 .83 .89 80 3360 8700 22 30 140 148 0 1239 531 708 .578 1119 588 1.73 .447 -.791 -1.163
11 734 686 242 437 492 249 704 568 261 506 462 131 0 0 332 526 135 378 88 38 71 13 741 593 1.976 .506 .284 2.05 .88 3.08 52 367 .95 .73 80 3520 8690 21 29 156 164 0 736 469 267 .543 609 141 1.842 .304 -.881 -1.717
12 627 597 242 390 385 207 560 503 253 451 318 113 0 0 364 442 121 337 74 32 57 16 592 431 1.86 .538 .355 3.18 .76 7.41 69 376 .98 .62 90 3660 8690 20 29 169 178 0 640 418 222 .577 540 121 1.734 .381 -.794 -1.392
13 893 715 235 359 658 356 908 696 251 416 673 337 0 0 301 472 125 328 96 50 88 23 1014 1010 1.848 .541 .501 .8 .69 .58 52 326 .82 .87 80 3810 8690 21 29 185 193 0 767 385 382 .58 747 361 1.723 .537 -.785 -.897
14 963 657 235 345 728 312 1033 593 252 408 798 248 0 0 398 449 128 319 90 39 87 17 1040 1046 2.333 .429 .311 .71 .5 .59 69 338 .7 .85 90 3930 8690 20 29 196 205 0 705 370 335 .46 636 266 2.175 .333 -1.121 -1.585
15 631 505 220 360 411 145 610 355 237 422 390 -5 0 0 262 514 119 335 86 27 72 11 556 385 2.834 .353 null 1.83 .92 2.68 112 260 .81 .54 120 4100 8690 19 31 212 224 0 542 386 156 .378 381 -5 2.643 null -1.402 null
16 2115 1195 241 356 1874 839 2191 1006 266 426 1950 650 0 0 861 766 151 358 97 67 91 48 2713 2600 2.234 .448 .333 .59 .45 .91 69 309 .57 .95 90 4230 8690 20 29 226 235 0 1282 382 900 .48 1079 697 2.082 .358 -1.058 -1.484
17 1218 830 237 408 981 422 1246 779 276 471 1009 371 0 0 415 571 195 354 98 52 90 19 1403 1380 2.325 .43 .368 .67 .45 .67 52 303 .71 .85 80 4390 8690 21 29 243 251 0 890 438 453 .461 836 398 2.167 .394 -1.116 -1.342
18 1098 725 244 377 854 348 1025 701 255 445 781 324 0 0 268 510 135 357 100 48 98 23 1202 1105 2.454 .407 .415 .76 .72 .53 52 378 .68 .78 80 4520 8680 20 28 256 264 0 778 404 373 .437 752 348 2.288 .445 -1.194 -1.168
19 2210 1507 226 358 1984 1149 2190 1535 243 432 1964 1177 0 0 801 774 129 342 100 81 98 69 3133 3141 1.727 .579 .599 .72 .6 .79 52 382 .67 .96 80 4690 8690 21 29 273 281 0 1616 384 1232 .621 1646 1262 1.61 .643 -.687 -.638
20 742 690 225 394 517 296 744 701 242 463 519 307 0 0 291 472 129 352 95 43 81 16 813 826 1.747 .573 .592 1.28 .72 1.46 37 380 .93 .82 70 4820 8680 20 27 286 293 0 740 423 317 .614 752 329 1.628 .634 -.704 -.656

Total number of rows: 41568

Table truncated, full table size 9477 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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