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Sample GSM287479 Query DataSets for GSM287479
Status Public on May 08, 2008
Title SV471_1
Sample type RNA
 
Channel 1
Source name CRG
Organism Homo sapiens
Characteristics CRG
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name SV471_1
Organism Homo sapiens
Characteristics SV471_1
Disease State: seminal vesicle
Individual: #3
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 = 1160, 6000; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Max,,Thompson
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 = 38.38; Parameter Scan Time = 09:14:46; Parameter PMT Volts = 650; Parameter Scan Date = 2004-08-04; Parameter Pixel Size = 10; Parameter Laser on time = 179842; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.48; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson
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 = 38.38; Parameter Scan Time = 09:14:46; Parameter PMT Volts = 660; Parameter Scan Date = 2004-08-04; Parameter Pixel Size = 10; Parameter Laser on time = 544646; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.84; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Max,,Thompson
Description Image: http://smd.stanford.edu/MicroArray/gifs/2004-08/54649.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 May 07, 2008
Last update date May 07, 2008
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 GPL6313
Series (1)
GSE11376 Candidate prostate cancer genes through comparative expression-profiling of seminal vesicle

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
1 654 194 156 85 498 109 693 184 158 91 537 99 0 0 172 56 34 35 100 92 100 75 607 636 4.569 .219 .184 .201 .207 1.939 52 312 .19 .472 90 1440 6350 30 39 23 32 0 192 84 108 .216 182 98 4.626 .182 -2.21 -2.457
2 1256 561 150 82 1106 479 1279 536 153 86 1129 454 0 0 611 242 39 33 100 100 100 100 1585 1583 2.309 .433 .402 .452 .434 1.461 52 290 .388 .86 90 1570 6350 30 39 36 45 0 554 81 473 .428 529 448 2.338 .397 -1.225 -1.332
3 3361 1936 140 89 3221 1847 3431 1943 146 93 3291 1854 0 0 1475 882 38 35 100 100 100 100 5068 5145 1.744 .573 .563 .563 .574 1.384 80 402 .567 .929 100 1730 6350 30 40 52 62 0 1912 88 1824 .566 1919 1831 1.766 .556 -.82 -.846
4 664 179 145 87 519 92 692 171 150 91 547 84 0 0 203 57 37 41 100 75 100 50 611 631 5.641 .177 .154 .162 .188 1.78 32 197 .16 .432 70 1860 6350 31 38 66 73 0 177 86 91 .175 169 83 5.711 .152 -2.514 -2.721
5 1283 771 143 84 1140 687 1260 783 148 88 1117 699 0 0 534 357 35 39 100 98 100 98 1827 1816 1.659 .603 .626 .569 .57 1.457 80 411 .605 .878 100 2020 6340 29 39 81 91 0 762 83 679 .595 773 690 1.68 .618 -.748 -.694
6 633 174 140 89 493 85 679 161 147 94 539 72 0 0 174 64 38 35 100 75 100 50 578 611 5.8 .172 .134 .141 .152 1.902 32 197 .156 .36 70 2150 6340 30 37 95 102 0 172 88 84 .17 159 71 5.872 .132 -2.554 -2.922
7 1959 1195 137 87 1822 1108 2020 1251 140 90 1883 1164 0 0 581 297 39 34 100 100 100 100 2930 3047 1.644 .608 .618 .627 .605 1.336 52 315 .581 .92 90 2300 6350 30 39 109 118 0 1180 86 1094 .601 1236 1150 1.665 .611 -.735 -.712
8 858 696 132 81 726 615 891 693 134 87 759 612 0 0 338 292 30 34 98 98 98 97 1341 1371 1.18 .847 .806 .856 .862 1.476 80 369 .821 .86 110 2450 6350 29 40 123 134 0 687 80 607 .837 684 604 1.195 .796 -.257 -.328
9 774 339 132 90 642 249 797 340 134 96 665 250 0 0 302 136 31 37 98 92 97 90 891 915 2.578 .388 .376 .371 .384 2.069 80 334 .369 .799 100 2600 6340 29 39 139 149 0 335 89 246 .383 336 247 2.61 .371 -1.384 -1.429
10 829 423 136 89 693 334 916 433 137 94 780 344 0 0 320 165 33 38 98 96 96 90 1027 1124 2.075 .482 .441 .472 .468 1.492 52 278 .469 .862 90 2740 6340 29 38 153 162 0 418 88 330 .476 428 340 2.101 .436 -1.071 -1.199
11 2823 5142 130 90 2693 5052 2877 5145 131 97 2747 5055 0 0 1586 2690 30 38 100 100 100 100 7745 7802 .533 1.876 1.84 2.139 1.869 1.844 80 337 1.846 .941 100 2890 6350 30 40 168 178 0 5079 89 4990 1.853 5082 4993 .54 1.818 .89 .862
12 9223 29616 125 91 9098 29525 9175 26879 129 101 9050 26788 0 0 4742 14050 32 43 100 100 100 100 38623 35838 .308 3.245 2.96 3.389 3.218 1.29 80 404 3.217 .958 110 3030 6340 28 39 181 192 0 29252 90 29163 3.205 26549 26459 .312 2.924 1.68 1.548
13 1315 952 126 83 1189 869 1362 964 129 92 1236 881 0 0 365 304 29 41 100 100 100 100 2058 2117 1.368 .731 .713 .716 .718 1.28 52 289 .716 .91 90 3170 6340 29 38 196 205 0 940 82 858 .722 952 870 1.385 .704 -.47 -.506
14 843 712 127 87 716 625 833 720 130 91 706 633 0 0 200 223 31 35 100 100 100 100 1341 1339 1.146 .873 .897 .846 .878 1.325 80 367 .886 .89 100 3330 6340 29 39 212 222 0 703 86 617 .862 711 625 1.16 .886 -.214 -.175
15 1337 579 127 88 1210 491 1381 598 130 94 1254 510 0 0 497 215 34 37 100 98 100 98 1701 1764 2.464 .406 .407 .397 .396 1.425 80 335 .395 .914 100 3470 6340 29 39 226 236 0 572 87 485 .401 591 504 2.495 .402 -1.319 -1.316
16 8446 13228 129 92 8317 13136 8704 13602 134 99 8575 13510 0 0 5115 7009 37 41 100 100 100 100 21453 22085 .633 1.579 1.576 1.7 1.585 1.315 80 362 1.515 .967 100 3620 6340 29 39 241 251 0 13066 91 12975 1.56 13435 13344 .641 1.556 .642 .638
17 1759 1615 128 95 1631 1520 1502 1428 140 107 1374 1333 0 0 986 861 75 60 100 100 98 98 3151 2707 1.073 .932 .97 .983 .96 1.465 80 364 .908 .953 100 3770 6340 29 39 256 266 0 1595 94 1501 .921 1410 1317 1.086 .958 -.12 -.062
18 702 294 127 86 575 208 747 278 129 93 620 192 0 0 262 124 32 39 97 93 96 86 783 812 2.764 .362 .31 .34 .349 1.837 80 310 .349 .757 100 3920 6340 29 39 271 281 0 290 85 205 .357 275 190 2.799 .306 -1.485 -1.709
19 2422 2088 123 87 2299 2001 2363 2229 127 92 2240 2142 0 0 1288 984 34 34 100 100 100 100 4300 4382 1.149 .87 .956 .949 .864 1.474 80 373 .835 .942 110 4060 6330 27 38 284 295 0 2062 86 1976 .86 2202 2116 1.163 .945 -.218 -.082
20 1848 1098 126 88 1722 1010 1675 1125 136 95 1549 1037 0 0 877 502 94 57 100 100 97 98 2732 2586 1.705 .587 .669 .588 .562 1.421 80 338 .572 .927 100 4210 6340 29 39 300 310 0 1085 87 998 .579 1111 1024 1.726 .661 -.788 -.597

Total number of rows: 41472

Table truncated, full table size 9086 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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