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Sample GSM281397 Query DataSets for GSM281397
Status Public on Jul 18, 2008
Title SHFy119|CRvs.Panc217|
Sample type RNA
 
Channel 1
Source Name Common Reference
Organism(s) Homo sapiens
Characteristics Common Reference
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source Name Panc217
Organism(s) Homo sapiens
Characteristics Panc217
Extracted molecule total RNA
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 Image Origin = 1880, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Murali,,Bashyam
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.87; Parameter Scan Time = 10:30:43; Parameter PMT Volts = 500; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46857; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.52; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 30.87; Parameter Scan Time = 10:30:43; Parameter PMT Volts = 500; Parameter Scan Date = 2004-09-10; Parameter Pixel Size = 10; Parameter Laser on time = 46902; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.49; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Murali,,Bashyam
Description Simple annotation: tumor, Pancreas
Image: http://smd.stanford.edu/MicroArray/gifs/2005-10/64453.gif
Tissue type: Pancreatic
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 Apr 11, 2008
Contact name Kevin Kwei
E-mail(s) kakwei@stanford.edu
Phone 650-7361989
Fax 650-7360073
Organization name Stanford
Lab CCSR Rm 3240
Street address 269 Campus Dr.
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL6735
Series (1)
GSE11152 Genomic profiling identifies GATA6 as a candidate oncogene amplified in pancreatobiliary cancer

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
1 680 396 273 391 407 5 678 387 279 392 405 -4 0 0 102 88 63 88 100 19 100 3 412 401 81.4 .012 null .21 .17 .17 86 324 -1 -1 100 2400 5920 39 49 47 57 0 512 506 6 .016 500 -5 62.953 null -5.976 null
2 871 454 286 405 585 49 865 453 289 405 579 48 0 0 175 97 66 87 100 31 100 11 634 627 11.939 .084 .083 .17 .17 .14 80 255 .53 .69 100 2550 5920 39 49 62 72 0 587 524 63 .108 586 62 9.233 .107 -3.207 -3.222
3 1760 1557 286 390 1474 1167 1782 1534 289 394 1496 1144 0 0 490 344 60 87 100 100 100 100 2641 2640 1.263 .792 .765 .82 .78 .21 70 273 .88 .99 90 2690 5920 39 48 76 85 0 2013 504 1509 1.024 1984 1479 .977 .989 .034 -.016
4 627 428 284 396 343 32 625 418 286 407 341 22 0 0 113 106 55 97 100 25 99 6 375 363 10.719 .093 .065 .29 .25 .22 80 271 .69 .56 100 2840 5920 39 49 91 101 0 553 512 41 .121 540 28 8.29 .083 -3.051 -3.583
5 633 1263 293 408 340 855 643 1222 292 414 350 814 0 0 129 382 58 94 99 100 96 100 1195 1164 .398 2.515 2.326 2.71 2.56 1.41 69 334 1.99 .98 90 2980 5910 38 47 105 114 0 1633 528 1106 3.252 1580 1053 .308 3.007 1.701 1.588
6 649 406 287 408 362 -2 637 395 306 417 350 -13 0 0 112 112 278 117 78 14 4 4 360 337 null null null .34 .19 .44 69 356 -1 -1 90 3130 5910 38 47 120 129 0 525 528 -3 null 511 -17 null null null null
7 853 1589 296 407 557 1182 825 1525 361 425 529 1118 0 0 192 437 591 147 36 100 0 100 1739 1647 .471 2.122 2.113 2.19 2.17 .71 80 313 1.86 .99 100 3280 5920 39 49 135 145 0 2055 526 1528 2.744 1972 1446 .364 2.733 1.456 1.45
8 630 598 281 399 349 199 631 584 285 404 350 185 0 0 127 154 65 99 100 72 95 45 548 535 1.754 .57 .529 .75 .63 .65 86 269 .95 .93 100 3430 5920 39 49 150 160 0 773 516 257 .737 755 239 1.356 .683 -.44 -.549
9 916 764 266 403 650 361 923 749 269 409 657 346 0 0 156 158 56 96 100 96 100 87 1011 1003 1.801 .555 .527 .58 .55 .3 112 221 .84 .97 120 3570 5920 38 50 163 175 0 988 521 467 .718 968 447 1.393 .681 -.478 -.554
10 604 423 263 397 341 26 622 417 268 412 359 20 0 0 98 100 56 100 98 22 98 5 367 379 13.115 .076 .056 .31 .23 .3 124 243 .71 .37 120 3710 5920 38 50 177 189 0 547 513 34 .099 539 26 10.143 .072 -3.342 -3.795
11 2363 1486 265 391 2098 1095 2357 1494 271 403 2092 1103 0 0 370 251 55 97 100 100 100 100 3193 3195 1.916 .522 .527 .53 .51 .15 97 273 .63 .99 110 3860 5920 38 49 192 203 0 1921 506 1416 .675 1932 1426 1.482 .682 -.567 -.553
12 10012 12591 260 402 9752 12189 11313 14143 269 406 11053 13741 0 0 3365 3958 64 95 100 100 100 100 21941 24794 .8 1.25 1.243 1.31 1.25 .44 124 275 1.26 1 120 4010 5920 38 50 207 219 0 16281 520 15761 1.616 18287 17768 .619 1.607 .693 .685
13 531 480 258 393 273 87 514 470 271 397 256 77 0 0 109 121 68 89 99 45 94 17 360 333 3.138 .319 .301 .6 .4 .55 69 315 .92 .79 90 4160 5930 40 49 223 232 -50 621 508 112 .412 608 100 2.427 .389 -1.279 -1.362
14 1553 1166 262 398 1291 768 1554 1175 271 402 1292 777 0 0 232 221 68 96 100 100 100 100 2059 2069 1.681 .595 .601 .6 .61 .18 97 334 .76 .99 110 4300 5920 38 49 236 247 0 1508 515 993 .769 1519 1005 1.3 .778 -.379 -.363
15 538 423 268 414 270 9 524 423 276 415 256 9 0 0 101 104 70 91 99 22 93 3 279 265 30 .033 .035 .34 .29 .3 69 300 .79 .26 90 4450 5930 40 49 252 261 -50 547 535 12 .043 547 12 23.201 .045 -4.536 -4.459
16 13888 18847 263 416 13625 18431 15554 21028 268 422 15291 20612 0 0 6351 7910 63 90 100 100 100 100 32056 35903 .739 1.353 1.348 1.48 1.39 .53 124 264 1.36 .99 120 4590 5920 38 50 265 277 0 24370 538 23832 1.749 27190 26652 .572 1.743 .807 .802
17 1085 2435 261 430 824 2005 1067 2401 288 468 806 1971 0 0 212 365 239 387 100 100 98 100 2829 2777 .411 2.433 2.445 2.54 2.56 .65 104 266 2.24 .99 110 4740 5920 38 49 280 291 0 3149 556 2593 3.146 3105 2549 .318 3.162 1.654 1.661
18 389 299 272 439 117 -140 399 293 294 472 127 -146 0 0 62 80 219 358 4 0 0 0 -23 -19 null null null .45 .24 .66 69 317 .78 .92 90 4890 5930 40 49 296 305 -50 387 568 -181 null 379 -189 null null null null
19 2728 1862 270 455 2458 1407 2735 1887 272 470 2465 1432 0 0 535 402 64 128 100 99 100 98 3865 3897 1.747 .572 .581 .57 .57 .15 115 255 .69 .99 120 5030 5920 38 50 309 321 0 2408 588 1819 .74 2440 1852 1.351 .751 -.434 -.413
20 1683 1039 262 460 1421 579 1700 1027 267 453 1438 567 0 0 303 185 64 100 100 100 100 100 2000 2005 2.454 .407 .394 .42 .41 .17 112 241 .62 .97 120 5180 5920 38 50 324 336 0 1343 595 749 .527 1328 733 1.898 .51 -.925 -.972

Total number of rows: 41472

Table truncated, full table size 9033 Kbytes.




Supplementary data files not provided
Raw data included within Sample table
Processed data included within Sample table
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