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Sample GSM39991 Query DataSets for GSM39991
Status Public on Feb 21, 2005
Title Fallopian tube 2386
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Fallopian tube 2386
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-04/15160.gif
Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-12/36421.gif
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 = 31.00; Parameter Scan Time = 12:36:25; Parameter PMT Volts = 680; Parameter Scan Date = 2002-12-13; Parameter Pixel Size = 10; Parameter Laser on time = 44776; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 2.80; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Radha,,Shyamsundar
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 = 31.00; Parameter Scan Time = 12:36:25; Parameter PMT Volts = 700; Parameter Scan Date = 2002-12-13; Parameter Pixel Size = 10; Parameter Laser on time = 263771; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.15; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Radha,,Shyamsundar
^SAMPLE: GSM39991
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
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 GPL1826
Series (1)
GSE2193 Normal_human_tissues

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
VALUE same as UNF_VALUE but with flagged values removed
LOG_RAT2N_MEDIAN 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
UNF_VALUE 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

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 VALUE LOG_RAT2N_MEDIAN UNF_VALUE
1 432 249 163 120 269 129 443 250 167 118 280 130 0 0 82 95 40 40 96 84 96 65 398 410 2.085 .48 .464 .44 .5 2.144 32 188 .586 .65 70 1620 8400 76 83 42 49 0 268 129 139 .516 269 140 1.938 .5 -.954 -1.001 -.954
2 583 377 166 106 417 271 585 391 167 109 419 285 0 0 158 119 41 36 100 98 100 94 688 704 1.539 .65 .68 .618 .717 1.84 52 265 .638 .85 80 1760 8400 76 84 56 64 0 406 114 292 .699 421 307 1.43 .732 -.516 -.45 -.516
3 1045 534 163 105 882 429 968 510 165 110 805 405 0 0 422 165 40 38 100 100 100 100 1311 1210 2.056 .486 .503 .521 .49 1.732 32 210 .411 .83 70 1910 8400 76 83 71 78 0 575 113 462 .523 549 436 1.91 .541 -.934 -.885 -.934
4 444 209 162 104 282 105 455 214 166 109 293 110 0 0 127 72 41 47 100 81 96 53 387 403 2.686 .372 .375 .343 .423 2.633 32 221 .359 .63 70 2060 8390 75 82 86 93 0 225 112 113 .401 230 118 2.496 .404 -1.319 -1.308 -1.319
5 732 1419 163 104 569 1315 712 1482 170 115 549 1378 0 0 155 407 78 102 100 100 100 100 1884 1927 .433 2.311 2.51 2.263 2.234 1.527 52 317 2.462 .87 90 2200 8400 75 84 99 108 0 1527 112 1415 2.487 1595 1483 .402 2.701 1.314 1.434 1.314
6 386 221 156 109 230 112 383 213 162 123 227 104 0 0 96 83 88 115 92 42 71 7 342 331 2.054 .487 .458 .457 .421 2.704 52 251 .431 .55 80 2350 8400 76 84 115 123 0 238 117 121 .524 229 112 1.908 .493 -.932 -1.02 -.932
7 800 527 148 102 652 425 796 482 149 115 648 380 0 0 203 220 48 56 100 96 100 96 1077 1028 1.534 .652 .586 .585 .591 1.888 32 207 .684 .8 70 2500 8390 75 82 130 137 0 567 110 457 .701 519 409 1.426 .631 -.512 -.664 -.512
8 436 287 157 104 279 183 412 280 157 107 255 176 0 0 110 65 45 44 100 98 98 94 462 431 1.525 .656 .69 .665 .625 1.868 52 246 .568 .72 80 2640 8400 76 84 144 152 0 309 112 197 .706 301 189 1.417 .743 -.503 -.429 -.503
9 516 790 158 106 358 684 506 803 209 113 348 697 0 0 119 173 534 63 5 100 0 100 1042 1045 .523 1.911 2.003 1.964 1.984 1.499 52 306 2.023 .8 90 2780 8400 75 84 157 166 0 850 114 736 2.056 864 750 .486 2.155 1.04 1.108 1.04
10 452 232 160 111 292 121 414 210 228 120 254 99 0 0 168 94 641 69 3 68 0 37 413 353 2.413 .414 .39 .425 .395 2.43 32 211 .391 .64 70 2940 8390 75 82 174 181 0 250 119 130 .446 226 107 2.242 .419 -1.165 -1.253 -1.165
11 1277 980 162 113 1115 867 1267 980 266 397 1105 867 0 0 216 179 1414 3252 7 0 0 0 1982 1972 1.286 .778 .785 .777 .789 1.292 52 315 .783 .94 90 3090 8400 75 84 188 197 0 1055 122 933 .837 1055 933 1.195 .844 -.257 -.244 -.257
12 1757 3874 174 119 1583 3755 1771 4050 407 749 1597 3931 0 0 647 1364 1823 4192 31 40 0 0 5338 5528 .422 2.372 2.461 2.416 2.545 1.485 32 193 2.539 .9 70 3210 8390 75 82 201 208 0 4169 128 4041 2.553 4358 4230 .392 2.649 1.352 1.405 1.352
13 476 426 169 113 307 313 480 416 202 201 311 303 0 0 134 119 223 528 70 2 16 0 620 614 .981 1.02 .974 1.086 1.048 1.793 80 377 1.378 .8 100 3370 8400 75 85 216 226 0 458 122 337 1.097 448 326 .911 1.048 .134 .068 .134
14 491 268 164 107 327 161 478 275 166 111 314 168 0 0 95 70 41 41 100 92 100 86 488 482 2.031 .492 .535 .457 .505 1.82 52 291 .458 .7 90 3520 8390 74 83 231 240 0 288 115 173 .53 296 181 1.887 .576 -.916 -.796 -.916
15 1574 2821 166 106 1408 2715 838 1773 168 120 672 1667 0 0 2953 4658 44 119 96 100 93 100 4123 2339 .519 1.928 2.481 2.568 2.375 1.981 80 309 1.757 .85 100 3670 8400 75 85 246 256 0 3036 114 2922 2.075 1908 1794 .482 2.67 1.053 1.417 1.053
16 4030 8781 165 110 3865 8671 4138 8936 175 139 3973 8826 0 0 1446 2634 95 241 97 100 97 100 12536 12799 .446 2.243 2.221 2.485 2.181 1.992 80 325 2.258 .94 100 3810 8400 75 85 260 270 0 9450 118 9331 2.414 9616 9498 .414 2.391 1.272 1.257 1.272
17 634 1349 165 116 469 1233 618 1338 327 304 453 1222 0 0 138 388 1484 1497 0 17 0 0 1702 1675 .38 2.629 2.698 2.554 2.627 1.47 52 289 1.076 .75 90 3960 8390 74 83 275 284 0 1452 125 1327 2.829 1440 1315 .353 2.903 1.5 1.538 1.5
18 218 142 164 104 54 38 179 130 350 148 15 26 0 0 124 65 1680 393 0 0 0 0 92 41 1.421 .704 1.733 .775 .896 3.485 52 223 .47 .41 80 4110 8380 74 82 291 299 -50 153 112 41 .757 140 28 1.321 1.865 .899 -.401
19 1452 2206 164 105 1288 2101 1532 2299 168 114 1368 2194 0 0 462 633 53 72 98 98 96 98 3389 3562 .613 1.631 1.604 1.683 1.581 2.148 80 334 1.644 .93 100 4250 8390 74 84 304 314 0 2374 113 2261 1.755 2474 2361 .57 1.726 .812 .787 .812
20 955 927 161 111 794 816 983 888 170 129 822 777 0 0 224 218 54 129 100 100 100 100 1610 1599 .973 1.028 .945 1.036 1.005 1.461 52 282 1.064 .88 90 4390 8390 74 83 318 327 0 998 119 878 1.106 956 836 .904 1.017 .145 .025 .145

Total number of rows: 43104

Table truncated, full table size 9570 Kbytes.




Supplementary data files not provided
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