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Sample GSM91644 Query DataSets for GSM91644
Status Public on Jan 11, 2006
Title SKTZF16_T2_T2
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 SKTZF16_T2_T2 total RNA
Organism Homo sapiens
Characteristics SKTZF16_T2_T2 total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35545.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 1529 921 210 134 1319 787 1489 848 218 143 1279 714 0 0 378 314 50 58 100 100 100 100 2106 1993 1.676 .597 .558 .577 .549 1.477 32 149 .575 .87 60 2060 9320 33 39 31 37 0 1084 158 926 .702 998 840 1.425 .657 -.511 -.607
2 18373 27488 221 151 18152 27337 21681 31939 229 156 21460 31788 0 0 9215 12917 60 60 98 100 98 100 45489 53248 .664 1.506 1.481 1.813 1.531 1.999 52 342 1.492 .97 90 2210 9310 30 39 44 53 0 32339 178 32161 1.772 37575 37398 .564 1.743 .825 .801
3 5759 4198 215 152 5544 4046 5854 4003 252 156 5639 3851 0 0 3556 2760 341 64 93 96 90 96 9590 9490 1.37 .73 .683 .82 .761 2.036 32 213 .723 .92 70 2350 9320 32 39 59 66 0 4939 179 4760 .859 4709 4531 1.165 .803 -.22 -.316
4 5077 2042 208 149 4869 1893 5296 1964 214 152 5088 1815 0 0 1798 871 79 56 100 100 100 100 6762 6903 2.572 .389 .357 .362 .392 1.494 32 204 .388 .94 70 2510 9320 32 39 75 82 0 2402 175 2227 .457 2311 2135 2.186 .42 -1.128 -1.253
5 5941 7635 218 141 5723 7494 6079 7800 227 148 5861 7659 0 0 2644 3201 73 54 100 100 98 100 13217 13520 .764 1.309 1.307 1.41 1.336 1.752 52 279 1.302 .95 80 2650 9310 31 39 89 97 0 8982 166 8816 1.541 9176 9011 .649 1.537 .623 .62
6 4389 2310 219 146 4170 2164 4551 2409 231 155 4332 2263 0 0 877 553 63 59 100 100 100 100 6334 6595 1.927 .519 .522 .51 .519 1.303 32 166 .458 .9 60 2790 9310 32 38 104 110 0 2718 172 2546 .611 2834 2662 1.638 .615 -.712 -.702
7 7293 3696 225 143 7068 3553 8252 3764 269 151 8027 3621 0 0 4158 1956 571 60 94 100 92 100 10621 11648 1.989 .503 .451 .575 .501 1.841 52 274 .481 .97 80 2940 9310 31 39 118 126 0 4348 168 4180 .591 4428 4260 1.691 .531 -.758 -.914
8 1965 6007 225 144 1740 5863 2182 6377 235 153 1957 6233 0 0 956 3023 63 64 96 100 96 100 7603 8190 .297 3.37 3.185 3.591 3.362 1.57 52 275 3.467 .95 80 3090 9310 31 39 133 141 0 7067 169 6898 3.964 7502 7333 .252 3.747 1.987 1.906
9 1872 1170 222 150 1650 1020 1882 1169 230 150 1660 1019 0 0 446 248 59 53 100 100 100 100 2670 2679 1.618 .618 .614 .625 .634 1.397 52 306 .586 .93 90 3230 9310 30 39 146 155 0 1376 176 1200 .727 1375 1199 1.375 .722 -.459 -.47
10 1275 806 211 144 1064 662 1271 800 220 155 1060 656 0 0 457 346 57 63 96 93 96 90 1726 1716 1.607 .622 .619 .646 .585 2.667 32 207 .619 .86 70 3370 9310 31 38 161 168 0 948 169 779 .732 941 772 1.366 .728 -.45 -.458
11 6372 12060 203 152 6169 11908 6843 12382 204 158 6640 12230 0 0 1841 2717 54 65 100 100 100 100 18077 18870 .518 1.93 1.842 2.003 1.857 1.324 52 337 1.896 .96 90 3520 9310 30 39 175 184 0 14188 179 14009 2.271 14567 14388 .44 2.167 1.183 1.116
12 14482 18189 200 154 14282 18035 14317 18631 205 156 14117 18477 0 0 12129 14232 49 60 100 100 98 96 32317 32594 .792 1.263 1.309 1.464 1.281 1.93 52 265 1.228 .97 80 3670 9310 31 39 191 199 0 21399 181 21218 1.486 21919 21738 .673 1.54 .571 .623
13 3776 17207 209 160 3567 17047 3947 17480 302 189 3738 17320 0 0 879 3520 1037 210 100 100 94 100 20614 21058 .209 4.779 4.633 4.838 4.892 1.226 52 313 4.746 .78 90 3810 9310 30 39 204 213 0 20244 188 20055 5.622 20565 20376 .178 5.451 2.491 2.447
14 1203 1041 201 156 1002 885 1185 1064 216 172 984 908 0 0 305 350 78 110 100 100 100 98 1887 1892 1.132 .883 .923 .856 .862 1.556 52 324 .903 .89 90 3960 9310 30 39 219 228 0 1225 184 1041 1.039 1252 1068 .962 1.086 .055 .118
15 1191 935 193 142 998 793 1213 987 203 151 1020 845 0 0 314 235 56 61 100 100 98 100 1791 1865 1.259 .795 .828 .815 .799 1.492 52 313 .766 .92 90 4110 9310 30 39 234 243 0 1100 167 933 .935 1161 994 1.07 .975 -.097 -.037
16 23496 27199 183 139 23313 27060 25433 29369 284 152 25250 29230 0 0 7866 8433 1477 61 100 100 98 100 50373 54480 .862 1.161 1.158 1.185 1.162 1.274 52 326 1.132 .97 90 4250 9310 30 39 248 257 0 31999 164 31835 1.366 34552 34388 .732 1.362 .449 .446
17 7231 10796 173 156 7058 10640 8325 11421 192 176 8152 11265 0 0 2986 4762 111 105 100 100 100 100 17698 19417 .663 1.508 1.382 1.519 1.487 1.405 52 265 1.535 .97 80 4400 9310 31 39 264 272 0 12701 184 12518 1.774 13436 13253 .564 1.626 .827 .701
18 381 322 189 159 192 163 226 169 346 179 37 10 0 0 446 398 1833 104 1 26 0 17 355 47 1.178 .849 .27 .956 .807 3.231 52 264 .888 .83 80 4550 9310 31 39 279 287 -50 379 187 192 .999 199 12 1.001 .318 -.002 -1.653
19 10553 15102 188 156 10365 14946 11031 15880 192 160 10843 15724 0 0 2188 3003 48 65 100 100 100 100 25311 26567 .693 1.442 1.45 1.451 1.462 1.164 52 312 1.434 .98 90 4700 9310 30 39 293 302 0 17767 184 17584 1.696 18682 18499 .589 1.706 .763 .771
20 5464 4603 190 150 5274 4453 5584 4712 195 155 5394 4562 0 0 1422 1102 50 61 100 100 100 100 9727 9956 1.184 .844 .846 .852 .846 1.256 52 255 .82 .96 80 4850 9310 31 39 309 317 0 5415 176 5239 .993 5544 5367 1.007 .995 -.01 -.007

Total number of rows: 43104

Table truncated, full table size 9717 Kbytes.




Supplementary data files not provided
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