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Sample GSM281390 Query DataSets for GSM281390
Status Public on Jul 18, 2008
Title SHGU49|CRvs.Panc219|
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 Panc 219
Organism(s) Homo sapiens
Characteristics Panc 219
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 = 2120, 5760; 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 = 29.41; Parameter Scan Time = 09:47:16; Parameter PMT Volts = 470; Parameter Scan Date = 2005-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 69889; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.66; 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 = 29.41; Parameter Scan Time = 09:47:16; Parameter PMT Volts = 500; Parameter Scan Date = 2005-12-08; Parameter Pixel Size = 10; Parameter Laser on time = 69934; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [94858]; Parameter Laser Power = 3.46; 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/2006-01/66379.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 GPL6736
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
1 303 91 71 55 232 36 308 89 72 56 237 34 0 0 58 24 15 13 100 83 100 65 268 271 6.444 .155 .143 .16 .16 .1 69 398 .31 .94 90 2500 6150 34 43 33 42 0 115 69 45 .196 112 43 5.114 .181 -2.354 -2.468
2 426 170 72 55 354 115 435 168 73 56 363 113 0 0 65 41 14 13 100 98 100 95 469 476 3.078 .325 .311 .32 .34 .09 44 350 .41 .99 70 2650 6150 35 42 49 56 0 214 69 145 .409 212 142 2.443 .392 -1.288 -1.35
3 1260 696 71 55 1189 641 1301 700 72 55 1230 645 0 0 267 163 13 12 100 100 100 100 1830 1875 1.855 .539 .524 .6 .54 .46 69 384 .56 .99 90 2790 6150 34 43 62 71 0 877 69 808 .679 882 813 1.472 .661 -.558 -.598
4 298 83 70 55 228 28 296 83 71 55 226 28 0 0 41 22 13 12 100 77 100 64 256 254 8.143 .123 .124 .15 .14 .08 44 399 .29 .94 70 2940 6160 36 43 78 85 0 105 69 35 .155 105 35 6.462 .156 -2.692 -2.679
5 275 170 71 55 204 115 288 177 71 55 217 122 0 0 66 53 13 12 100 94 97 93 319 339 1.774 .564 .562 .63 .56 .44 69 411 .62 .97 90 3090 6150 34 43 92 101 0 214 69 145 .71 223 154 1.408 .708 -.493 -.497
6 258 71 71 55 187 16 267 68 71 55 196 13 0 0 52 16 13 12 97 54 97 32 203 209 11.688 .086 .066 .12 .11 .1 37 367 .3 .9 70 3240 6150 35 42 108 115 -50 89 69 20 .108 86 16 9.274 .084 -3.213 -3.581
7 355 221 70 56 285 165 354 222 70 56 284 166 0 0 66 35 12 12 100 100 100 100 450 450 1.727 .579 .585 .64 .59 .48 104 257 .62 .99 110 3370 6160 34 45 119 130 0 279 71 208 .73 280 209 1.371 .737 -.455 -.441
8 237 236 71 56 166 180 241 237 71 56 170 181 0 0 48 51 13 13 98 99 98 99 346 351 .922 1.084 1.065 1.15 1.1 .48 96 267 .99 .98 110 3510 6160 34 45 133 144 0 297 71 227 1.366 299 228 .732 1.342 .45 .424
9 202 123 71 55 131 68 201 119 72 56 130 64 0 0 39 33 14 12 100 98 100 93 199 194 1.926 .519 .492 .56 .55 .3 80 311 .62 .97 100 3670 6160 35 45 150 160 0 155 69 86 .654 150 81 1.529 .62 -.612 -.689
10 260 111 72 55 188 56 266 110 72 56 194 55 0 0 39 29 14 12 100 97 100 85 244 249 3.357 .298 .284 .31 .3 .15 60 332 .45 .97 80 3820 6150 35 43 166 174 0 140 69 71 .375 139 69 2.664 .357 -1.414 -1.485
11 490 267 76 59 414 208 484 269 78 61 408 210 0 0 74 58 20 20 100 99 100 99 622 618 1.99 .502 .515 .51 .53 .18 70 309 .55 .98 90 3960 6160 35 44 179 188 0 336 74 262 .633 339 265 1.579 .649 -.659 -.625
12 1906 2722 74 59 1832 2663 1955 3040 76 62 1881 2981 0 0 761 1226 19 19 100 100 100 100 4495 4862 .688 1.454 1.585 1.43 1.49 .49 44 377 1.44 .99 70 4110 6160 36 43 195 202 0 3430 74 3356 1.832 3831 3757 .546 1.997 .873 .998
13 151 143 72 58 79 85 151 141 72 58 79 83 0 0 37 31 13 12 97 99 93 96 164 162 .929 1.076 1.051 1.4 1.18 1.49 69 384 .94 .97 90 4250 6160 35 44 208 217 0 180 73 107 1.356 178 105 .738 1.324 .439 .405
14 334 152 72 58 262 94 323 149 72 59 251 91 0 0 41 36 13 13 100 98 100 98 356 342 2.787 .359 .363 .35 .35 .14 60 328 .47 .98 80 4400 6160 36 44 224 232 0 192 73 118 .452 188 115 2.212 .457 -1.145 -1.13
15 178 137 74 58 104 79 179 137 76 61 105 79 0 0 30 33 17 19 100 96 100 88 183 184 1.316 .76 .752 .84 .79 .49 112 233 .78 .96 120 4540 6160 34 46 236 248 0 173 73 100 .957 173 100 1.045 .948 -.063 -.077
16 2709 3018 79 63 2630 2955 2844 3172 82 66 2765 3109 0 0 825 885 20 19 99 100 99 100 5585 5874 .89 1.124 1.124 1.87 1.15 4.01 137 257 1.12 .99 130 4680 6160 33 46 249 262 0 3803 79 3724 1.416 3997 3918 .706 1.417 .502 .503
17 314 472 76 63 238 409 317 480 78 65 241 417 0 0 71 87 17 19 100 100 99 100 647 658 .582 1.718 1.73 1.99 1.79 1.55 70 287 1.48 .99 90 4830 6170 36 45 266 275 0 595 79 515 2.166 605 525 .462 2.18 1.115 1.125
18 112 101 74 61 38 40 109 100 76 64 35 39 0 0 24 26 16 20 85 82 57 48 78 74 .95 1.053 1.114 2.29 1.03 5.79 60 358 .9 .94 80 4990 6160 36 44 283 291 0 127 77 50 1.327 126 49 .754 1.404 .408 .49
19 1225 1195 74 59 1151 1136 1222 1249 75 61 1148 1190 0 0 241 325 15 15 100 100 100 100 2287 2338 1.013 .987 1.037 .99 1.03 .26 70 346 1 .99 90 5120 6160 35 44 295 304 0 1506 74 1432 1.244 1574 1500 .804 1.306 .315 .385
20 679 321 75 58 604 263 701 314 76 59 626 256 0 0 110 70 14 13 100 100 100 100 867 882 2.297 .435 .409 .43 .43 .09 44 397 .49 .99 70 5280 6160 36 43 312 319 0 405 73 331 .549 396 323 1.822 .515 -.866 -.956

Total number of rows: 41472

Table truncated, full table size 8500 Kbytes.




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