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Sample GSM91643 Query DataSets for GSM91643
Status Public on Jan 11, 2006
Title GVNBPHF11_T24_C
Sample type RNA
 
Channel 1
Source name Stratagene universal RNA
Organism Homo sapiens
Characteristics Stratagene universal RNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name GVNBPHF11_T24_C total RNA
Organism Homo sapiens
Characteristics GVNBPHF11_T24_C total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35625.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 Jan 10, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3341
Series (1)
GSE4010 Molecular targets of doxazosin in human prostatic stromal cells

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
1 332 396 111 218 221 178 332 382 113 228 221 164 0 0 92 130 24 92 100 75 96 43 399 385 1.242 .805 .742 .868 .952 1.686 32 160 1.241 .62 60 1860 9180 27 33 27 33 0 450 248 202 .915 434 186 1.093 .843 -.128 -.246
2 2830 510 110 203 2720 307 2955 515 113 216 2845 312 0 0 1202 205 24 91 100 84 100 65 3027 3157 8.86 .113 .11 .099 .109 1.937 52 279 .106 .79 80 2000 9180 26 34 40 48 0 580 231 349 .128 585 355 7.797 .125 -2.963 -3.004
3 2360 1937 123 221 2237 1716 2287 1933 153 249 2164 1712 0 0 1248 902 169 140 100 100 91 100 3953 3876 1.304 .767 .791 .811 .798 1.4 12 98 .684 .96 50 2140 9170 26 31 55 60 0 2201 251 1950 .872 2197 1945 1.147 .899 -.198 -.154
4 843 319 110 208 733 111 825 311 113 223 715 103 0 0 318 98 26 86 96 56 96 31 844 818 6.604 .151 .144 .164 .177 2.131 32 170 .099 .35 60 2300 9170 26 32 71 77 0 363 236 126 .172 353 117 5.811 .164 -2.539 -2.611
5 1161 2431 110 206 1051 2225 1107 2469 137 232 997 2263 0 0 407 799 267 147 98 100 88 100 3276 3260 .472 2.117 2.27 2.145 2.195 1.513 52 269 2.166 .94 80 2450 9180 26 34 85 93 0 2763 234 2528 2.406 2806 2572 .416 2.579 1.266 1.367
6 480 409 111 208 369 201 472 426 117 229 361 218 0 0 134 125 38 137 100 68 100 31 570 579 1.836 .545 .604 .424 .487 2.936 32 207 1.418 .53 70 2580 9170 25 32 98 105 0 465 236 228 .619 484 248 1.616 .686 -.692 -.543
7 1913 1163 111 208 1802 955 2045 1187 114 218 1934 979 0 0 594 339 24 85 100 100 100 100 2757 2913 1.887 .53 .506 .526 .533 1.507 32 225 .503 .91 70 2730 9180 26 33 113 120 0 1322 236 1085 .602 1349 1113 1.66 .575 -.732 -.798
8 684 426 112 209 572 217 677 421 114 225 565 212 0 0 162 120 24 90 100 84 100 62 789 777 2.636 .379 .375 .347 .352 1.907 32 176 .246 .5 60 2880 9180 27 33 129 135 0 484 238 247 .431 478 241 2.32 .426 -1.214 -1.23
9 508 458 108 211 400 247 513 462 112 215 405 251 0 0 104 145 24 74 100 82 100 75 647 656 1.619 .618 .62 .534 .65 2.079 52 286 .799 .74 80 3040 9180 26 34 144 152 0 520 240 281 .702 525 285 1.425 .704 -.511 -.506
10 361 345 113 205 248 140 338 350 115 210 225 145 0 0 83 93 24 81 100 58 100 41 388 370 1.771 .565 .644 .448 .517 2.372 12 104 .924 .54 50 3170 9180 27 32 158 163 0 392 233 159 .641 398 165 1.559 .732 -.64 -.449
11 1528 2689 108 203 1420 2486 1479 2706 111 205 1371 2503 0 0 383 581 31 77 100 100 100 100 3906 3874 .571 1.751 1.826 1.771 1.717 1.273 52 308 1.744 .95 80 3330 9180 26 34 173 181 0 3056 231 2825 1.989 3075 2844 .503 2.075 .992 1.053
12 5974 5331 109 200 5865 5131 6376 5704 125 220 6267 5504 0 0 2252 2257 67 103 100 100 100 100 10996 11771 1.143 .875 .878 .825 .835 1.338 32 205 .888 .97 70 3460 9170 25 32 186 193 0 6058 227 5831 .994 6482 6255 1.006 .998 -.008 -.003
13 746 6526 109 200 637 6326 762 6840 114 219 653 6640 0 0 231 1953 41 99 100 100 100 100 6963 7293 .101 9.931 10.168 10.34 10.104 1.441 52 342 10.435 .93 90 3610 9180 25 34 200 209 0 7416 227 7189 11.285 7773 7545 .089 11.555 3.496 3.53
14 354 380 109 209 245 171 358 381 111 227 249 172 0 0 82 128 23 94 100 71 100 44 416 421 1.433 .698 .691 .668 .729 2.283 52 293 1.09 .44 80 3760 9180 26 34 216 224 0 432 238 194 .793 433 195 1.261 .785 -.334 -.349
15 501 715 111 220 390 495 495 706 113 232 384 486 0 0 82 161 24 87 100 100 100 100 885 870 .788 1.269 1.266 1.23 1.216 1.458 52 250 1.386 .85 80 3920 9180 26 34 232 240 0 813 250 563 1.442 802 552 .693 1.438 .528 .524
16 6933 9414 108 217 6825 9197 7561 10147 110 226 7453 9930 0 0 2419 3181 25 82 100 100 100 100 16022 17383 .742 1.348 1.332 1.392 1.327 1.433 52 311 1.325 .97 90 4050 9180 25 34 244 253 0 10698 247 10451 1.531 11531 11284 .653 1.514 .615 .598
17 1871 1752 112 235 1759 1517 1836 1702 114 243 1724 1467 0 0 766 675 23 87 100 100 100 100 3276 3191 1.16 .862 .851 .855 .836 1.43 52 268 .861 .95 80 4200 9180 26 34 260 268 0 1991 267 1724 .98 1934 1667 1.02 .967 -.029 -.048
18 145 244 116 239 29 5 120 226 118 241 4 -13 0 0 78 103 27 91 30 21 17 9 34 -9 5.8 .172 null 2.055 2.146 5.404 52 266 8.444 .18 80 4350 9170 25 33 275 283 -50 277 272 6 .196 257 null 5.104 null -2.352 null
19 3971 2144 114 221 3857 1923 4215 2164 115 221 4101 1943 0 0 1144 605 26 79 100 100 100 100 5780 6044 2.006 .499 .474 .497 .478 1.341 52 312 .479 .95 90 4500 9180 25 34 289 298 0 2436 251 2185 .567 2459 2208 1.765 .538 -.82 -.893
20 1922 1297 107 214 1815 1083 2021 1323 110 227 1914 1109 0 0 537 395 26 84 100 100 100 100 2898 3023 1.676 .597 .579 .586 .596 1.351 52 242 .585 .93 80 4650 9180 26 34 305 313 0 1474 243 1231 .678 1503 1260 1.475 .658 -.561 -.603

Total number of rows: 43104

Table truncated, full table size 9421 Kbytes.




Supplementary data files not provided

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