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Sample GSM350548 Query DataSets for GSM350548
Status Public on Jul 10, 2009
Title shfk237_sr|MDAMB157 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 MDAMB157 genomic DNA
Organism Homo sapiens
Characteristics Breast Tumor Cell Line MDAMB157 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 = 2320, 6000; 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 = 2004-05-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 610; Parameter Laser on time = 33580; Parameter Laser Power = 3.47; Parameter Scan Time = 12:39:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.62; 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 = 2004-05-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 650; Parameter Scan Power = 100; Parameter Laser on time = 33623; Parameter Laser Power = 3.53; Parameter Scan Time = 12:39:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4000B [94858]; Parameter Focus Position = 0; Parameter Scan Temperature = 29.62; Performer: Jessica,,Kao
Description Simple annotation: Breast, aCGH cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2004-07/54202.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 GPL7778
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 2207 2960 550 623 1657 2337 2279 2869 557 701 1729 2246 0 0 737 1009 217 431 94 100 94 97 3994 3975 .709 1.41 1.299 1.41 1.37 .63 32 450 1.35 .97 60 2560 6230 20 26 21 27 0 2795 588 2207 1.332 2710 2121 .751 1.227 .414 .295
2 4386 4478 548 627 3838 3851 4304 4298 555 714 3756 3671 0 0 1401 1467 224 446 100 97 100 97 7689 7427 .997 1.003 .977 1.04 .96 .41 32 420 1.04 .98 60 2690 6230 20 26 34 40 0 4229 592 3637 .948 4059 3467 1.055 .923 -.078 -.116
3 1309 1193 527 637 782 556 883 959 547 707 356 322 0 0 945 877 217 453 59 35 43 24 1338 678 1.406 .711 .904 2.18 .88 3.97 37 455 .93 .91 70 2830 6220 18 25 47 54 0 1127 602 525 .671 906 304 1.489 .854 -.575 -.227
4 1764 2057 499 649 1265 1408 1680 2031 522 730 1181 1382 0 0 939 786 222 446 88 88 81 75 2673 2563 .898 1.113 1.17 2.65 1.27 6.49 32 440 1.13 .96 60 2980 6230 20 26 63 69 0 1943 613 1330 1.051 1918 1305 .951 1.105 .072 .144
5 1728 2043 509 715 1219 1328 1502 1726 545 774 993 1011 0 0 791 944 227 444 94 81 84 63 2547 2004 .918 1.089 1.018 2.58 1.22 6.73 32 428 1.18 .95 60 3130 6230 20 26 78 84 0 1929 675 1254 1.029 1630 955 .972 .962 .041 -.057
6 2007 2256 516 693 1491 1563 2030 2384 550 738 1514 1691 0 0 735 1051 235 414 90 86 90 67 3054 3205 .954 1.048 1.117 1.24 1.1 .77 21 484 1.17 .97 50 3270 6220 19 24 92 97 0 2131 654 1476 .99 2251 1597 1.01 1.055 -.014 .077
7 1248 1542 517 666 731 876 1063 1211 539 736 546 545 0 0 746 1093 216 416 63 56 56 41 1607 1091 .834 1.198 .998 1.55 1.25 1.43 32 457 1.23 .96 60 3410 6220 19 25 106 112 0 1456 629 827 1.132 1144 515 .884 .943 .179 -.085
8 1656 2035 533 709 1123 1326 1092 1938 548 771 559 1229 0 0 1183 1429 213 440 86 67 52 57 2449 1788 .847 1.181 2.199 1.86 .92 2.02 21 464 1.18 .97 50 3570 6220 19 24 122 127 0 1922 670 1252 1.115 1830 1161 .897 2.076 .157 1.054
9 2197 1922 545 754 1652 1168 2172 1783 563 794 1627 1029 0 0 621 622 217 426 100 92 98 65 2820 2656 1.414 .707 .632 .84 .67 .78 52 386 .88 .96 80 3710 6230 19 27 135 143 0 1815 712 1103 .668 1684 972 1.498 .597 -.583 -.743
10 3704 2709 558 738 3146 1971 3932 2704 598 810 3374 1966 0 0 1014 1003 319 472 100 92 100 83 5117 5340 1.596 .627 .583 .66 .61 .38 52 372 .75 .98 80 3860 6230 19 27 150 158 0 2558 697 1861 .592 2554 1857 1.69 .55 -.757 -.862
11 1713 1730 556 737 1157 993 1779 1745 600 800 1223 1008 0 0 499 615 324 454 92 83 87 54 2150 2231 1.165 .858 .824 1.02 .88 .86 52 383 1.02 .95 80 4000 6230 19 27 164 172 0 1634 696 938 .811 1648 952 1.234 .778 -.303 -.361
12 2520 2325 555 736 1965 1589 2427 2310 587 776 1872 1574 0 0 740 708 226 443 100 95 100 84 3554 3446 1.237 .809 .841 .94 .83 .61 37 428 .93 .97 70 4150 6230 19 26 179 186 0 2196 695 1501 .764 2182 1487 1.309 .794 -.389 -.333
13 2029 1754 563 728 1466 1026 1995 1714 583 773 1432 986 0 0 610 752 218 426 100 77 98 52 2492 2418 1.429 .7 .689 .87 .63 .75 52 380 .87 .92 80 4300 6230 19 27 194 202 0 1657 688 969 .661 1619 931 1.513 .65 -.597 -.621
14 2795 3043 557 715 2238 2328 2810 2951 583 829 2253 2236 0 0 810 1001 225 480 99 97 99 91 4566 4489 .961 1.04 .992 1.3 1.19 1.52 69 361 1.08 .98 90 4440 6230 18 27 207 216 0 2874 675 2199 .982 2787 2112 1.018 .937 -.026 -.093
15 1215 1227 575 770 640 457 1170 1049 594 831 595 279 0 0 465 647 232 486 75 39 64 14 1097 874 1.4 .714 .469 1.11 .76 1.09 69 359 1 .84 90 4590 6240 19 28 222 231 0 1159 727 432 .674 991 263 1.483 .443 -.568 -1.175
16 7962 5797 570 746 7392 5051 8278 5960 578 791 7708 5214 0 0 2293 1948 230 430 100 100 100 100 12443 12922 1.463 .683 .676 .68 .71 .22 52 357 .75 .99 80 4740 6230 19 27 238 246 0 5475 705 4770 .645 5629 4924 1.55 .639 -.632 -.646
17 3156 3616 566 694 2590 2922 3226 3592 581 762 2660 2898 0 0 985 1478 228 415 100 94 94 90 5512 5558 .886 1.128 1.089 1.33 1.16 1.23 52 372 1.16 .96 80 4880 6230 19 27 252 260 0 3415 655 2760 1.065 3392 2737 .939 1.029 .092 .041
18 3424 2861 556 688 2868 2173 3496 2810 576 764 2940 2122 0 0 805 1115 220 443 100 98 100 88 5041 5062 1.32 .758 .722 .79 .77 .44 52 373 .87 .97 80 5030 6230 19 27 267 275 0 2702 650 2052 .716 2654 2004 1.398 .682 -.483 -.553
19 8064 8804 544 710 7520 8094 9082 9129 553 786 8538 8419 0 0 3136 3335 227 474 100 97 100 97 15614 16957 .929 1.076 .986 1.19 1.1 .59 37 425 1.09 .99 70 5160 6220 18 25 280 287 0 8315 671 7644 1.017 8622 7951 .984 .931 .024 -.103
20 3200 2775 519 698 2681 2077 3213 2619 545 763 2694 1921 0 0 947 1064 230 473 100 96 100 90 4758 4615 1.291 .775 .713 .91 .69 .74 52 396 .88 .96 80 5320 6230 19 27 296 304 0 2621 659 1962 .732 2473 1814 1.367 .673 -.451 -.57

Total number of rows: 41472

Table truncated, full table size 9581 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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