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Sample GSM40000 Query DataSets for GSM40000
Status Public on Feb 21, 2005
Title Fallopian tube 2184
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Fallopian tube 2184
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-12/36429.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 = 30.20; Parameter Scan Time = 10:57:24; Parameter PMT Volts = 625; Parameter Scan Date = 2002-12-14; Parameter Pixel Size = 10; Parameter Laser on time = 45116; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.83; 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 = 30.20; Parameter Scan Time = 10:57:24; Parameter PMT Volts = 715; Parameter Scan Date = 2002-12-14; Parameter Pixel Size = 10; Parameter Laser on time = 264111; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.10; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Radha,,Shyamsundar
 
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
1 405 372 131 125 274 247 378 307 133 138 247 182 0 0 122 347 31 72 100 78 98 61 521 429 1.109 .901 .737 .652 .786 2.023 52 314 1.741 .74 90 1650 8350 74 83 92 101 0 476 160 316 1.153 393 233 .868 .942 .205 -.086 .205
2 500 370 135 121 365 249 498 353 135 127 363 232 0 0 86 120 29 46 100 100 100 98 614 595 1.466 .682 .639 .632 .678 1.557 52 254 .751 .83 80 1790 8350 75 83 107 115 0 473 155 318 .872 451 297 1.147 .817 -.197 -.291 -.197
3 608 393 135 123 473 270 607 381 139 129 472 258 0 0 173 131 36 47 100 98 100 92 743 730 1.752 .571 .547 .531 .524 1.6 52 254 .61 .88 80 1940 8350 75 83 122 130 0 502 157 345 .73 487 330 1.37 .699 -.454 -.517 -.454
4 370 285 134 127 236 158 361 280 138 129 227 153 0 0 88 88 33 46 100 90 96 78 394 380 1.494 .669 .674 .586 .666 2.033 52 244 .789 .77 80 2080 8350 75 83 136 144 0 364 162 202 .856 358 196 1.168 .862 -.224 -.215 -.224
5 617 769 132 116 485 653 628 765 137 119 496 649 0 0 128 199 30 44 100 100 100 100 1138 1145 .743 1.346 1.308 1.337 1.34 1.362 52 301 1.387 .93 90 2220 8340 73 82 149 158 0 983 148 835 1.721 978 830 .581 1.673 .784 .742 .784
6 393 266 149 113 244 153 406 266 151 128 257 153 0 0 65 79 38 79 100 84 96 40 397 410 1.595 .627 .595 .567 .588 1.849 32 220 .757 .72 70 2370 8340 74 81 165 172 0 340 144 196 .802 340 196 1.247 .761 -.319 -.394 -.319
7 561 422 146 119 415 303 575 418 151 126 429 299 0 0 117 133 38 62 100 100 100 92 718 728 1.37 .73 .697 .687 .698 1.526 52 314 .856 .85 90 2520 8350 74 83 179 188 0 540 152 387 .933 534 382 1.071 .891 -.099 -.166 -.099
8 432 362 144 120 288 242 442 348 147 127 298 228 0 0 79 99 32 52 100 98 100 92 530 526 1.19 .84 .765 .795 .838 1.641 52 301 .946 .83 90 2660 8340 73 82 193 202 0 463 153 309 1.074 445 291 .931 .978 .103 -.032 .103
9 416 670 149 119 267 551 426 680 151 124 277 561 0 0 93 199 36 46 98 100 96 98 818 838 .485 2.064 2.025 2.07 2.028 1.492 80 436 2.205 .9 110 2810 8340 72 83 207 218 0 857 152 704 2.638 869 717 .379 2.589 1.4 1.373 1.4
10 417 337 157 126 260 211 402 340 163 128 245 214 0 0 94 71 42 52 100 100 100 90 471 459 1.232 .812 .873 .805 .796 1.585 32 192 .895 .79 70 2950 8340 74 81 223 230 0 431 161 270 1.038 435 274 .964 1.117 .053 .159 .053
11 762 810 162 127 600 683 806 831 167 136 644 704 0 0 215 247 37 63 100 100 100 100 1283 1348 .878 1.138 1.093 1.148 1.124 1.367 80 387 1.155 .93 100 3100 8350 74 84 237 247 0 1036 162 873 1.455 1062 900 .687 1.398 .541 .483 .541
12 1681 1574 155 120 1526 1454 1744 1660 157 125 1589 1540 0 0 558 595 31 49 100 100 100 100 2980 3129 1.05 .953 .969 .911 .936 1.328 52 246 .98 .97 80 3250 8340 74 82 253 261 0 2012 153 1859 1.218 2122 1969 .821 1.239 .285 .309 .285
13 487 426 158 122 329 304 505 421 161 126 347 299 0 0 84 123 33 50 100 98 100 96 633 646 1.082 .924 .862 .865 .918 1.558 52 301 1.026 .87 90 3390 8340 73 82 266 275 0 545 156 389 1.181 538 382 .846 1.102 .24 .14 .24
14 412 275 162 115 250 160 407 273 164 121 245 158 0 0 101 86 34 47 97 92 96 76 410 403 1.563 .64 .645 .605 .644 2.135 80 340 .65 .76 100 3540 8350 74 84 281 291 0 352 147 205 .818 349 202 1.222 .825 -.289 -.278 -.289
15 675 1299 166 118 509 1181 699 1310 168 127 533 1192 0 0 132 244 35 47 100 100 100 100 1690 1725 .431 2.32 2.236 2.365 2.231 1.321 80 375 2.367 .94 110 3680 8350 73 84 294 305 0 1661 151 1510 2.966 1675 1524 .337 2.859 1.569 1.516 1.569
16 2624 3798 167 129 2457 3669 2729 3935 172 136 2562 3806 0 0 706 1051 38 48 100 100 100 100 6126 6368 .67 1.493 1.486 1.508 1.513 1.22 80 415 1.493 .98 110 3830 8350 73 84 309 320 0 4856 165 4691 1.909 5031 4866 .524 1.899 .933 .925 .933
17 536 986 166 123 370 863 522 944 167 132 356 821 0 0 97 321 33 46 100 100 100 100 1233 1177 .429 2.332 2.306 2.272 2.265 1.42 52 277 2.579 .9 90 3980 8340 73 82 325 334 0 1261 157 1103 2.982 1207 1050 .335 2.948 1.576 1.56 1.576
18 230 177 168 123 62 54 209 160 167 132 41 37 0 0 85 94 32 51 51 42 36 23 116 78 1.148 .871 .902 1.378 1.207 2.69 52 236 1.127 .64 80 4120 8340 74 82 340 348 -50 226 157 69 1.114 205 47 .898 1.154 .206 .155
19 1146 1018 168 128 978 890 1171 1047 170 137 1003 919 0 0 297 286 41 54 100 98 98 98 1868 1922 1.099 .91 .916 .899 .9 1.309 80 329 .904 .95 100 4270 8350 74 84 354 364 0 1302 164 1138 1.163 1339 1175 .86 1.171 .218 .228 .218
20 687 523 172 124 515 399 694 523 173 132 522 399 0 0 217 185 33 51 100 97 97 96 914 921 1.291 .775 .764 .767 .75 1.661 80 326 .767 .9 100 4410 8340 73 83 368 378 0 669 159 510 .991 669 510 1.01 .977 -.014 -.033 -.014

Total number of rows: 43104

Table truncated, full table size 9371 Kbytes.




Supplementary data files not provided
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