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Sample GSM91640 Query DataSets for GSM91640
Status Public on Jan 11, 2006
Title GVNBPHF11_T8_T
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_T8_T total RNA
Organism Homo sapiens
Characteristics GVNBPHF11_T8_T total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35624.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
1 614 420 166 180 448 240 609 429 165 185 443 249 0 0 276 137 41 74 93 84 93 71 688 692 1.867 .536 .562 .493 .491 1.868 32 160 .472 .77 60 1770 9460 19 25 18 24 0 433 186 247 .552 442 257 1.811 .579 -.857 -.787
2 4588 729 169 169 4419 560 4788 709 171 182 4619 540 0 0 1310 214 47 87 100 100 100 100 4979 5159 7.891 .127 .117 .126 .12 1.662 32 231 .113 .84 70 1920 9460 18 25 32 39 0 752 174 577 .131 731 557 7.654 .121 -2.936 -3.053
3 3459 2145 169 163 3290 1982 3431 2191 181 169 3262 2028 0 0 1784 844 64 87 100 100 100 100 5272 5290 1.66 .602 .622 .649 .667 1.628 12 104 .47 .88 50 2060 9450 18 23 47 52 0 2211 168 2043 .621 2259 2091 1.61 .641 -.687 -.642
4 1387 571 176 169 1211 402 1355 510 519 176 1179 341 0 0 481 209 2416 78 0 100 0 91 1613 1520 3.012 .332 .289 .321 .339 1.604 12 98 .326 .82 50 2210 9440 17 22 62 67 0 589 174 414 .342 526 352 2.922 .298 -1.547 -1.746
5 1549 4635 160 171 1389 4464 1472 4687 165 181 1312 4516 0 0 875 1820 41 85 96 100 96 100 5853 5828 .311 3.214 3.442 3.82 3.409 1.998 32 225 3.099 .88 70 2350 9460 18 25 75 82 0 4778 176 4602 3.313 4832 4656 .302 3.549 1.728 1.827
6 802 506 162 172 640 334 792 514 165 176 630 342 0 0 231 150 36 82 100 93 100 84 974 972 1.916 .522 .543 .496 .511 1.753 32 165 .524 .8 60 2510 9450 18 24 92 98 0 522 177 344 .538 530 353 1.859 .56 -.894 -.837
7 1830 1121 170 171 1660 950 1547 966 175 173 1377 795 0 0 1390 705 53 73 94 100 90 94 2610 2172 1.747 .572 .577 .676 .582 2.734 52 278 .51 .89 80 2650 9460 18 26 105 113 0 1156 176 979 .59 996 820 1.695 .595 -.761 -.749
8 1047 907 186 188 861 719 1137 875 791 240 951 687 0 0 376 373 5361 293 0 87 0 62 1580 1638 1.197 .835 .722 .866 .764 1.587 32 170 .849 .82 60 2800 9450 18 24 121 127 0 935 194 741 .861 902 708 1.162 .745 -.216 -.425
9 832 466 178 184 654 282 865 442 540 223 687 258 0 0 268 193 4133 236 0 55 0 11 936 945 2.319 .431 .376 .404 .381 2.038 52 287 .043 .75 80 2950 9460 18 26 135 143 0 480 190 291 .445 456 266 2.25 .387 -1.17 -1.369
10 735 326 163 166 572 160 783 316 170 173 620 150 0 0 143 87 40 70 100 83 100 50 732 770 3.575 .28 .242 .249 .273 1.846 12 104 .262 .61 50 3090 9450 18 23 150 155 0 336 171 165 .288 326 155 3.468 .249 -1.794 -2.003
11 1876 4048 170 165 1706 3883 1963 3927 180 185 1793 3762 0 0 900 1678 75 90 94 100 92 100 5589 5555 .439 2.276 2.098 2.599 2.222 2.062 52 306 2.24 .94 80 3230 9460 18 26 163 171 0 4173 170 4003 2.346 4048 3878 .426 2.163 1.23 1.113
12 4422 4892 170 175 4252 4717 2211 2368 219 183 2041 2193 0 0 4747 5185 737 85 71 90 51 88 8969 4234 .901 1.109 1.074 1.204 1.199 2.6 52 259 1.105 .93 80 3400 9460 18 26 180 188 0 5043 180 4863 1.144 2441 2261 .874 1.108 .194 .148
13 1342 6509 173 181 1169 6328 1482 6582 226 186 1309 6401 0 0 534 2226 747 82 75 100 30 100 7497 7710 .185 5.413 4.89 6.087 5.473 1.779 52 252 5.441 .94 80 3520 9460 18 26 192 200 0 6710 187 6524 5.581 6786 6599 .179 5.041 2.48 2.334
14 609 320 167 181 442 139 584 327 205 183 417 146 0 0 233 139 579 72 26 69 1 50 581 563 3.18 .314 .35 .4 .399 2.085 52 275 .018 .1 80 3680 9450 17 25 208 216 0 330 187 143 .324 337 151 3.084 .361 -1.625 -1.47
15 800 582 155 181 645 401 870 574 161 185 715 393 0 0 361 231 42 81 92 88 90 86 1046 1108 1.608 .622 .55 .559 .56 2.009 52 266 .612 .84 80 3820 9460 18 26 222 230 0 600 187 413 .641 592 405 1.56 .567 -.642 -.819
16 9985 14557 152 179 9833 14378 11051 15524 160 192 10899 15345 0 0 4078 5368 62 86 96 100 96 100 24211 26244 .684 1.462 1.408 1.438 1.404 1.613 52 339 1.471 .93 90 3970 9460 17 26 236 245 0 15007 185 14823 1.507 16004 15820 .663 1.451 .592 .538
17 2511 7215 150 172 2361 7043 2710 7636 154 183 2560 7464 0 0 1344 4352 40 77 98 100 92 100 9404 10024 .335 2.983 2.916 2.965 2.976 2.006 52 322 3.194 .95 90 4120 9450 16 25 251 260 0 7438 177 7261 3.075 7872 7695 .325 3.006 1.621 1.588
18 220 240 150 181 70 59 171 205 164 203 21 24 0 0 198 139 97 95 19 28 11 11 129 45 1.186 .843 1.143 1.755 1.7 3.852 52 246 .858 .55 80 4260 9450 17 25 266 274 -50 247 187 61 .869 211 25 1.151 1.178 -.203 .237
19 5775 4671 156 184 5619 4487 6464 5216 241 201 6308 5032 0 0 2695 2194 856 95 94 100 88 100 10106 11340 1.252 .799 .798 .81 .784 2.151 52 243 .798 .95 80 4410 9460 18 26 281 289 0 4815 190 4626 .823 5377 5188 1.215 .822 -.281 -.282
20 2549 1776 157 190 2392 1586 2459 1823 226 197 2302 1633 0 0 1292 845 815 88 88 98 69 96 3978 3935 1.508 .663 .709 .63 .657 2.368 52 266 .634 .91 80 4550 9460 18 26 295 303 0 1831 196 1635 .684 1879 1684 1.463 .731 -.549 -.451

Total number of rows: 43104

Table truncated, full table size 9546 Kbytes.




Supplementary data files not provided

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