NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM91638 Query DataSets for GSM91638
Status Public on Jan 11, 2006
Title GVNBPHF11_T8_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_T8_C total RNA
Organism Homo sapiens
Characteristics GVNBPHF11_T8_C total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35623.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
1 603 386 164 183 439 203 565 359 166 187 401 176 0 0 233 134 49 74 100 87 96 59 642 577 2.163 .462 .439 .441 .437 2.31 32 156 .454 .67 60 1920 9460 27 33 21 27 0 444 210 233 .532 413 202 1.881 .504 -.912 -.987
2 4535 747 163 177 4372 570 4744 734 165 188 4581 557 0 0 1345 221 41 83 100 100 100 93 4942 5138 7.67 .13 .122 .125 .127 1.429 32 224 .119 .88 70 2070 9460 26 33 35 42 0 859 203 655 .15 844 640 6.673 .14 -2.738 -2.839
3 3316 2429 163 177 3153 2252 3477 2636 168 191 3314 2459 0 0 1703 1103 80 100 100 100 91 91 5405 5773 1.4 .714 .742 .798 .719 1.505 12 98 .645 .96 50 2210 9440 25 30 50 55 0 2792 203 2589 .821 3030 2826 1.218 .853 -.285 -.23
4 1209 447 152 173 1057 274 1246 433 158 181 1094 260 0 0 495 162 37 74 100 87 100 71 1331 1354 3.858 .259 .238 .248 .278 2.066 32 170 .228 .73 60 2360 9450 26 32 65 71 0 514 199 315 .298 498 299 3.356 .273 -1.747 -1.872
5 1854 4827 157 182 1697 4645 1703 4558 161 191 1546 4376 0 0 779 1855 37 81 100 100 100 100 6342 5922 .365 2.737 2.831 2.946 2.732 1.601 32 227 2.666 .92 70 2500 9450 25 32 78 85 0 5548 209 5339 3.146 5239 5030 .318 3.253 1.654 1.702
6 950 590 165 171 785 419 825 580 170 181 660 409 0 0 357 222 41 73 100 96 100 90 1204 1069 1.874 .534 .62 .5 .518 1.962 32 170 .494 .81 60 2660 9450 26 32 95 101 0 678 197 482 .614 667 470 1.63 .712 -.705 -.489
7 2072 1182 172 173 1900 1009 2025 1038 176 184 1853 865 0 0 1462 730 48 83 96 96 92 92 2909 2718 1.883 .531 .467 .64 .601 2.377 52 287 .484 .9 80 2800 9450 25 33 108 116 0 1359 199 1160 .61 1193 994 1.638 .537 -.712 -.898
8 1136 1093 164 174 972 919 1162 990 166 188 998 816 0 0 436 461 40 80 100 96 96 96 1891 1814 1.058 .945 .818 1.019 .934 1.844 32 209 .952 .86 70 2950 9460 26 33 123 130 0 1256 200 1056 1.087 1138 938 .92 .94 .12 -.09
9 949 574 162 184 787 390 946 529 162 196 784 345 0 0 470 250 37 84 98 92 98 86 1177 1129 2.018 .496 .44 .48 .533 1.953 52 296 .402 .68 80 3090 9450 25 33 137 145 0 660 211 448 .57 608 397 1.756 .506 -.812 -.983
10 514 307 162 173 352 134 503 276 164 200 341 103 0 0 193 127 38 96 100 53 90 34 486 444 2.627 .381 .302 .384 .487 3.627 32 164 .366 .47 60 3250 9450 26 32 154 160 0 353 199 154 .438 317 118 2.285 .347 -1.192 -1.526
11 1920 4254 165 183 1755 4071 2001 4340 172 200 1836 4157 0 0 551 1424 42 85 100 100 100 100 5826 5993 .431 2.32 2.264 2.3 2.382 1.477 52 287 2.429 .95 80 3390 9450 25 33 167 175 0 4890 210 4679 2.666 4989 4778 .375 2.602 1.415 1.38
12 4089 4402 177 190 3912 4212 3005 3472 184 205 2828 3282 0 0 4030 4090 47 88 98 96 98 88 8124 6110 .929 1.077 1.161 1.19 1.15 2.218 52 264 1.042 .94 80 3540 9450 25 33 182 190 0 5060 218 4841 1.238 3991 3772 .808 1.334 .308 .416
13 1452 5831 182 194 1270 5637 1629 5786 187 204 1447 5592 0 0 574 1795 42 88 100 100 98 100 6907 7039 .225 4.439 3.865 5.139 4.464 1.738 52 314 4.425 .94 90 3680 9460 25 34 195 204 0 6702 223 6479 5.102 6651 6428 .196 4.442 2.351 2.151
14 713 390 178 185 535 205 740 391 184 195 562 206 0 0 196 127 45 80 96 84 96 62 740 768 2.61 .383 .367 .374 .416 2.029 32 206 .354 .62 70 3830 9460 26 33 211 218 0 448 213 236 .44 449 237 2.27 .421 -1.183 -1.247
15 811 617 170 188 641 429 842 648 176 199 672 460 0 0 189 211 42 87 98 94 98 88 1070 1132 1.494 .669 .685 .564 .608 2.017 52 277 .701 .81 80 3970 9450 25 33 225 233 0 709 216 493 .769 745 529 1.3 .787 -.378 -.346
16 11803 15788 160 188 11643 15600 12247 16493 167 198 12087 16305 0 0 4357 6149 38 81 100 100 100 100 27243 28392 .746 1.34 1.349 1.362 1.392 1.579 52 342 1.35 .95 90 4120 9450 24 33 239 248 0 18147 216 17931 1.54 18957 18741 .649 1.551 .623 .633
17 4042 3438 162 193 3880 3245 4302 3535 173 206 4140 3342 0 0 1387 1166 71 93 100 100 100 100 7125 7482 1.196 .836 .807 .853 .872 1.344 32 200 .83 .95 70 4260 9440 24 31 254 261 0 3952 222 3730 .961 4063 3841 1.04 .928 -.057 -.108
18 231 271 163 199 68 72 186 254 169 207 23 55 0 0 169 128 62 86 23 38 13 28 140 78 .944 1.059 2.391 1.675 1.893 5.076 52 278 1.075 .35 80 4400 9440 24 32 268 276 -50 311 229 83 1.217 292 63 .822 2.749 .283 1.459
19 6475 5265 160 195 6315 5070 7258 5741 164 200 7098 5546 0 0 1775 1820 37 80 100 100 100 100 11385 12644 1.246 .803 .781 .776 .852 1.41 52 263 .816 .96 80 4560 9450 25 33 284 292 0 6052 224 5828 .923 6599 6375 1.084 .898 -.116 -.155
20 3122 2302 172 193 2950 2109 3187 2175 173 204 3015 1982 0 0 1133 875 39 87 98 100 98 100 5059 4997 1.399 .715 .657 .713 .723 1.375 52 254 .715 .96 80 4700 9450 25 33 298 306 0 2646 222 2424 .822 2500 2278 1.217 .756 -.283 -.404

Total number of rows: 43104

Table truncated, full table size 9593 Kbytes.




Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap