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Sample GSM287478 Query DataSets for GSM287478
Status Public on May 08, 2008
Title SV340_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 SV340_1
Organism Homo sapiens
Characteristics SV340_1
Disease State: seminal vesicle
Individual: #1
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 = 720, 5440; 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 = 38.94; Parameter Scan Time = 09:17:23; Parameter PMT Volts = 650; Parameter Scan Date = 2004-07-09; Parameter Pixel Size = 10; Parameter Laser on time = 173755; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; 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 = 38.94; Parameter Scan Time = 09:17:23; Parameter PMT Volts = 790; Parameter Scan Date = 2004-07-09; Parameter Pixel Size = 10; Parameter Laser on time = 538559; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.01; 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/2004-07/53855.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
1 537 418 194 243 343 175 525 404 195 257 331 161 0 0 83 133 45 102 100 67 100 34 518 492 1.96 .51 .486 .401 .493 2.861 52 266 .674 .262 80 1160 5880 40 48 40 48 0 481 280 202 .588 465 185 1.702 .56 -.767 -.836
2 1533 1786 192 252 1341 1534 1699 1854 196 265 1507 1602 0 0 645 741 45 109 100 100 100 100 2875 3109 .874 1.144 1.063 1.184 1.143 1.487 52 265 1.145 .875 80 1300 5880 40 48 54 62 0 2057 290 1767 1.318 2135 1845 .759 1.224 .398 .292
3 6959 4105 198 270 6761 3835 6830 3836 204 284 6632 3566 0 0 2062 1355 43 111 100 100 100 100 10596 10198 1.763 .567 .538 .563 .563 1.311 80 480 .562 .918 110 1450 5880 38 49 67 78 0 4728 311 4417 .653 4418 4107 1.531 .619 -.614 -.691
4 619 458 197 254 422 204 637 440 201 270 440 186 0 0 167 137 43 109 100 84 96 37 626 626 2.069 .483 .423 .504 .571 2.155 32 161 .506 .293 60 1600 5890 42 48 85 91 0 528 293 235 .557 507 214 1.796 .487 -.845 -1.038
5 1944 935 192 264 1752 671 1930 917 198 279 1738 653 0 0 745 267 45 107 100 100 100 95 2423 2391 2.611 .383 .376 .391 .388 1.65 80 425 .348 .749 100 1750 5880 39 49 98 108 0 1077 304 773 .441 1056 752 2.267 .433 -1.181 -1.208
6 614 423 207 264 407 159 614 389 215 273 407 125 0 0 120 150 53 109 100 53 100 34 566 532 2.56 .391 .307 .34 .381 2.831 32 200 .523 .164 70 1900 5890 41 48 114 121 0 487 304 183 .45 448 144 2.222 .354 -1.152 -1.499
7 2289 1422 214 262 2075 1160 2288 1404 221 270 2074 1142 0 0 515 329 49 107 100 100 100 100 3235 3216 1.789 .559 .551 .553 .576 1.389 52 307 .53 .807 90 2030 5880 39 48 126 135 0 1638 302 1336 .644 1617 1315 1.553 .634 -.635 -.657
8 1226 884 223 260 1003 624 1242 852 228 276 1019 592 0 0 279 267 50 117 100 98 100 96 1627 1611 1.607 .622 .581 .585 .609 1.693 80 358 .604 .618 100 2180 5880 39 49 141 151 0 1018 299 719 .717 981 682 1.396 .669 -.481 -.58
9 832 559 223 243 609 316 844 567 224 267 621 324 0 0 213 216 47 121 97 75 97 60 925 945 1.927 .519 .522 .448 .532 2.427 80 330 .554 .415 100 2330 5890 40 50 156 166 0 644 280 364 .598 653 373 1.673 .601 -.743 -.735
10 654 1263 224 258 430 1005 652 1249 894 477 428 991 0 0 147 380 5658 1808 0 1 0 0 1435 1419 .428 2.337 2.315 2.342 2.166 1.561 80 333 .254 .566 100 2460 5880 39 49 169 179 0 1455 297 1158 2.692 1439 1141 .371 2.667 1.429 1.415
11 4596 3072 228 283 4368 2789 4801 3148 1033 523 4573 2865 0 0 1010 638 6089 1944 0 92 0 3 7157 7438 1.566 .639 .627 .642 .649 1.301 52 287 .596 .853 90 2610 5880 39 48 184 193 0 3538 326 3212 .735 3626 3300 1.36 .722 -.443 -.471
12 17864 31896 220 253 17644 31643 19814 32261 243 268 19594 32008 0 0 7140 12634 199 122 98 100 98 100 49287 51602 .558 1.793 1.634 1.885 1.812 1.62 80 392 1.818 .928 100 2760 5880 39 49 199 209 0 36738 291 36447 2.066 37158 36867 .484 1.882 1.047 .912
13 1063 2891 214 245 849 2646 1118 3009 217 260 904 2764 0 0 393 1108 49 102 98 100 96 100 3495 3668 .321 3.117 3.058 3.265 3.047 1.75 80 346 3.214 .857 100 2910 5880 39 49 214 224 0 3330 282 3048 3.59 3466 3184 .279 3.522 1.844 1.816
14 597 1310 211 244 386 1066 590 1293 214 259 379 1049 0 0 111 395 44 110 100 100 100 100 1452 1428 .362 2.762 2.768 2.655 2.817 1.533 80 401 3.147 .734 110 3050 5880 38 49 227 238 0 1509 281 1228 3.181 1489 1208 .314 3.188 1.669 1.673
15 2091 958 212 247 1879 711 2101 945 215 262 1889 698 0 0 467 269 46 118 100 100 100 97 2590 2587 2.643 .378 .37 .362 .369 1.586 80 402 .355 .717 110 3200 5880 38 49 242 253 0 1103 284 819 .436 1088 804 2.294 .426 -1.198 -1.232
16 12940 13075 215 250 12725 12825 14381 13503 219 261 14166 13253 0 0 4571 4910 47 104 100 100 100 100 25550 27419 .992 1.008 .936 .974 .99 1.494 80 355 1.016 .901 100 3350 5880 39 49 258 268 0 15060 288 14772 1.161 15553 15265 .861 1.078 .215 .108
17 2257 4049 210 243 2047 3806 2378 4037 215 251 2168 3794 0 0 776 1364 44 98 98 100 97 100 5853 5962 .538 1.859 1.75 1.975 1.904 1.825 80 350 1.918 .855 100 3500 5870 38 48 273 283 0 4664 280 4384 2.142 4650 4370 .467 2.016 1.099 1.011
18 672 1268 211 234 461 1034 654 1244 212 245 443 1010 0 0 164 398 42 98 100 98 100 98 1495 1453 .446 2.243 2.28 2.187 2.314 1.75 80 349 2.531 .704 100 3650 5870 38 48 288 298 0 1460 270 1191 2.583 1433 1163 .387 2.626 1.369 1.393
19 3699 2463 206 233 3493 2230 3721 2420 211 254 3515 2187 0 0 1056 665 54 112 100 100 100 100 5723 5702 1.566 .638 .622 .642 .646 1.371 80 381 .602 .843 110 3790 5880 38 49 301 312 0 2837 268 2569 .735 2787 2519 1.36 .717 -.444 -.481
20 3601 2106 203 236 3398 1870 3635 2024 206 250 3432 1788 0 0 985 652 55 111 100 100 100 100 5268 5220 1.817 .55 .521 .54 .549 1.379 80 346 .535 .825 100 3940 5880 39 49 317 327 0 2426 272 2154 .634 2331 2059 1.578 .6 -.658 -.737

Total number of rows: 41472

Table truncated, full table size 9207 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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