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Sample GSM91634 Query DataSets for GSM91634
Status Public on Jan 11, 2006
Title GVNBPHF11_T2_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_T2_C total RNA
Organism Homo sapiens
Characteristics GVNBPHF11_T2_C total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35621.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
1 616 354 212 168 404 186 620 335 216 177 408 167 0 0 139 130 56 69 96 81 96 62 590 575 2.172 .46 .409 .403 .429 2.353 32 201 .459 .61 70 2040 9240 32 39 40 47 0 389 185 204 .506 368 184 1.977 .45 -.983 -1.153
2 4016 574 212 187 3804 387 3913 564 216 189 3701 377 0 0 802 192 49 75 100 90 100 90 4191 4078 9.829 .102 .102 .099 .104 1.508 32 225 .101 .84 70 2190 9230 31 38 55 62 0 631 205 425 .112 620 414 8.945 .112 -3.161 -3.159
3 3111 1883 205 159 2906 1724 2930 1964 212 165 2725 1805 0 0 1861 1100 55 71 100 100 100 93 4630 4530 1.686 .593 .662 .581 .623 2.035 32 166 .572 .94 60 2340 9230 32 38 71 77 0 2069 175 1895 .652 2158 1984 1.534 .728 -.617 -.458
4 1146 437 220 177 926 260 1065 429 228 190 845 252 0 0 565 177 51 78 93 90 93 68 1186 1097 3.562 .281 .298 .32 .293 3.582 32 165 .236 .71 60 2480 9240 33 39 85 91 0 480 195 286 .309 471 277 3.241 .328 -1.696 -1.609
5 1944 5458 225 179 1719 5279 2035 5509 232 191 1810 5330 0 0 874 1985 48 77 98 100 96 100 6998 7140 .326 3.071 2.945 3.534 3.023 1.884 52 285 3.027 .93 80 2630 9240 32 40 99 107 0 5998 197 5801 3.375 6054 5857 .296 3.236 1.755 1.694
6 789 441 220 174 569 267 759 425 226 184 539 251 0 0 199 170 48 75 100 87 100 71 836 790 2.131 .469 .466 .432 .437 2.021 32 215 .462 .66 70 2780 9240 32 39 114 121 0 485 191 293 .516 467 276 1.939 .512 -.956 -.967
7 2969 1569 223 189 2746 1380 3096 1620 233 202 2873 1431 0 0 892 428 60 87 100 100 100 100 4126 4304 1.99 .503 .498 .512 .466 1.478 32 223 .465 .92 70 2920 9230 31 38 128 135 0 1724 208 1516 .552 1780 1573 1.811 .547 -.857 -.869
8 926 1207 223 181 703 1026 863 1228 228 195 640 1047 0 0 351 503 57 85 98 98 98 94 1729 1687 .685 1.459 1.636 1.43 1.394 1.917 52 288 1.521 .87 80 3070 9240 32 40 143 151 0 1326 199 1127 1.604 1349 1151 .624 1.798 .681 .846
9 962 521 221 177 741 344 991 503 220 189 770 326 0 0 185 182 48 88 100 92 100 80 1085 1096 2.154 .464 .423 .397 .436 2.117 52 318 .452 .74 90 3220 9240 31 40 157 166 0 573 195 378 .51 553 358 1.96 .465 -.971 -1.104
10 630 256 217 181 413 75 626 255 217 192 409 74 0 0 165 115 46 77 100 50 93 25 488 483 5.507 .182 .181 .213 .296 2.843 32 165 .223 .4 60 3360 9230 32 38 173 179 0 281 199 82 .2 280 81 5.011 .199 -2.325 -2.33
11 2315 5800 216 186 2099 5614 2330 5926 219 190 2114 5740 0 0 605 1580 51 78 100 100 100 100 7713 7854 .374 2.675 2.715 2.621 2.775 1.41 52 325 2.783 .95 90 3520 9240 31 40 187 196 0 6374 204 6169 2.939 6512 6308 .34 2.984 1.555 1.577
12 5732 6097 212 191 5520 5906 5423 5133 219 198 5211 4942 0 0 4720 4850 51 77 94 94 92 94 11426 10153 .935 1.07 .948 1.259 1.109 2.27 52 245 1.048 .93 80 3650 9240 32 40 201 209 0 6700 210 6490 1.176 5641 5431 .851 1.042 .234 .06
13 969 5451 224 193 745 5258 1037 6034 224 198 813 5841 0 0 257 1916 48 80 100 100 100 100 6003 6654 .142 7.058 7.185 6.926 7.172 1.436 52 325 7.823 .91 90 3800 9240 31 40 215 224 0 5990 212 5778 7.756 6631 6419 .129 7.895 2.955 2.981
14 665 349 219 167 446 182 669 353 223 180 450 186 0 0 106 123 47 73 100 78 100 59 628 636 2.451 .408 .413 .34 .414 2.412 52 328 .419 .61 90 3950 9250 32 41 230 239 0 384 184 200 .448 388 204 2.23 .454 -1.157 -1.139
15 814 454 218 175 596 279 842 435 222 190 624 260 0 0 196 159 45 76 98 90 98 80 875 884 2.136 .468 .417 .45 .425 1.877 52 239 .511 .75 80 4110 9250 33 41 247 255 0 499 192 307 .514 478 286 1.944 .458 -.959 -1.127
16 10507 13207 221 190 10286 13017 11120 13798 231 222 10899 13608 0 0 2726 3272 102 221 100 100 100 100 23303 24507 .79 1.266 1.249 1.273 1.251 1.253 52 314 1.261 .96 90 4240 9240 31 40 259 268 0 14513 209 14304 1.391 15163 14954 .719 1.372 .476 .456
17 2586 2699 203 179 2383 2520 2594 2936 217 214 2391 2757 0 0 1066 1156 109 237 100 98 100 96 4903 5148 .946 1.057 1.153 1.004 1.06 1.767 52 267 1.061 .94 80 4390 9240 32 40 275 283 0 2966 197 2769 1.162 3226 3030 .861 1.267 .217 .342
18 245 242 203 174 42 68 213 242 210 184 10 68 0 0 106 107 46 79 30 38 13 15 110 78 .618 1.619 6.8 1.903 1.829 4.674 52 266 2.838 .25 80 4540 9240 32 40 290 298 -50 266 191 75 1.779 266 75 .562 7.473 .831 2.902
19 5462 5556 208 197 5254 5359 5574 5848 213 201 5366 5651 0 0 1117 1302 44 81 100 100 100 100 10613 11017 .98 1.02 1.053 1.001 1.031 1.463 52 312 1.029 .95 90 4690 9250 32 41 304 313 0 6105 216 5889 1.121 6426 6210 .892 1.157 .165 .211
20 2503 1869 220 195 2283 1674 2486 1917 223 206 2266 1722 0 0 779 536 46 77 100 98 100 98 3957 3988 1.364 .733 .76 .714 .739 1.633 52 304 .707 .92 90 4840 9250 32 41 319 328 0 2054 214 1840 .806 2107 1892 1.241 .835 -.312 -.26

Total number of rows: 43104

Table truncated, full table size 9563 Kbytes.




Supplementary data files not provided
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