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Sample GSM91637 Query DataSets for GSM91637
Status Public on Jan 11, 2006
Title SKTZF16_T8_T1
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_T8_T1 total RNA
Organism Homo sapiens
Characteristics SKTZF16_T8_T1 total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35542.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
1 702 399 140 152 562 247 665 383 148 161 525 231 0 0 199 126 55 63 100 94 100 82 809 756 2.275 .44 .44 .436 .448 1.591 52 256 .393 .69 80 2110 9210 37 45 35 43 0 493 188 305 .543 473 285 1.843 .543 -.882 -.88
2 9464 5483 136 155 9328 5328 9430 5615 145 170 9294 5460 0 0 2507 1208 54 84 100 100 100 100 14656 14754 1.751 .571 .587 .578 .593 1.408 52 254 .543 .92 80 2250 9210 37 45 49 57 0 6769 191 6578 .705 6932 6741 1.418 .725 -.504 -.463
3 2815 1618 133 170 2682 1448 2911 1604 140 174 2778 1434 0 0 993 570 44 86 100 100 100 100 4130 4212 1.852 .54 .516 .537 .575 1.638 32 215 .526 .92 70 2400 9200 36 43 64 71 0 1998 210 1788 .667 1980 1770 1.5 .637 -.585 -.65
4 1741 742 145 160 1596 582 1741 781 152 165 1596 621 0 0 484 186 50 63 100 100 100 100 2178 2217 2.742 .365 .389 .362 .341 1.51 32 208 .322 .87 70 2540 9200 36 43 78 85 0 916 198 719 .45 964 767 2.221 .48 -1.151 -1.058
5 1963 3210 145 153 1818 3057 1988 3241 154 160 1843 3088 0 0 890 1110 54 63 100 100 100 100 4875 4931 .595 1.682 1.676 1.849 1.647 1.737 52 310 1.557 .91 90 2680 9210 36 45 91 100 0 3963 189 3774 2.076 4001 3812 .482 2.069 1.054 1.049
6 1400 578 147 159 1253 419 1447 625 157 166 1300 466 0 0 422 198 60 66 100 96 100 92 1672 1766 2.99 .334 .358 .315 .35 1.598 52 251 .324 .85 80 2840 9210 37 45 108 116 0 714 196 517 .413 772 575 2.422 .443 -1.276 -1.176
7 2464 1474 143 159 2321 1315 2663 1514 152 168 2520 1355 0 0 893 453 58 70 100 100 100 100 3636 3875 1.765 .567 .538 .576 .532 1.446 52 244 .509 .9 80 2980 9210 37 45 122 130 0 1820 196 1623 .699 1869 1673 1.43 .664 -.516 -.591
8 926 1264 144 151 782 1113 928 1321 153 161 784 1170 0 0 311 349 60 66 100 100 100 100 1895 1954 .703 1.423 1.492 1.473 1.436 1.534 52 270 1.369 .87 80 3120 9210 37 45 136 144 0 1560 186 1374 1.757 1631 1444 .569 1.842 .813 .882
9 870 500 139 158 731 342 889 481 149 165 750 323 0 0 233 133 46 70 100 96 100 94 1073 1073 2.137 .468 .431 .447 .426 1.676 52 312 .429 .79 90 3270 9210 36 45 150 159 0 617 195 422 .578 594 399 1.731 .532 -.792 -.911
10 663 306 144 152 519 154 642 304 150 163 498 152 0 0 188 114 47 65 100 78 100 56 673 650 3.37 .297 .305 .249 .342 2.455 32 152 .284 .56 60 3420 9210 38 44 167 173 0 378 188 190 .366 375 188 2.73 .377 -1.449 -1.408
11 2135 6493 140 171 1995 6322 2084 6448 156 187 1944 6277 0 0 577 1191 95 114 100 100 100 100 8317 8221 .316 3.169 3.229 3.261 3.203 1.328 52 311 3.096 .92 90 3550 9210 36 45 178 187 0 8016 211 7805 3.912 7960 7749 .256 3.986 1.968 1.995
12 8203 11136 144 162 8059 10974 8883 10520 163 187 8739 10358 0 0 4836 5169 108 117 98 100 94 100 19033 19097 .734 1.362 1.185 1.782 1.387 2.209 52 262 1.263 .92 80 3710 9210 37 45 195 203 0 13748 200 13548 1.681 12988 12788 .595 1.463 .749 .549
13 1885 6713 146 156 1739 6557 1969 6508 157 165 1823 6352 0 0 581 1995 53 65 100 100 100 100 8296 8175 .265 3.771 3.484 3.88 3.991 1.432 80 381 3.931 .94 110 3860 9220 36 47 208 219 0 8288 193 8095 4.655 8035 7842 .215 4.302 2.219 2.105
14 623 321 144 154 479 167 589 307 151 161 445 153 0 0 144 110 44 64 100 84 100 63 646 598 2.868 .349 .344 .333 .328 1.816 52 277 .358 .63 90 4000 9220 37 46 223 232 0 396 190 206 .43 379 189 2.323 .424 -1.216 -1.236
15 842 593 154 171 688 422 826 613 161 174 672 442 0 0 189 149 53 66 100 100 100 98 1110 1114 1.63 .613 .658 .591 .618 1.616 52 276 .586 .82 90 4150 9210 36 45 238 247 0 732 211 521 .757 757 546 1.321 .812 -.401 -.3
16 8568 13784 152 160 8416 13624 9153 13892 160 171 9001 13732 0 0 3861 4840 53 73 98 100 98 100 22040 22733 .618 1.619 1.526 1.851 1.566 1.798 80 341 1.564 .94 100 4290 9220 37 47 252 262 0 17017 198 16820 1.999 17151 16953 .5 1.883 .999 .913
17 4047 9832 146 168 3901 9664 4122 9725 153 176 3976 9557 0 0 1051 2015 56 70 100 100 100 100 13565 13533 .404 2.477 2.404 2.535 2.528 1.333 52 289 2.499 .94 90 4440 9210 36 45 267 276 0 12138 207 11931 3.058 12006 11799 .327 2.967 1.613 1.569
18 251 184 149 161 102 23 175 170 158 176 26 9 0 0 183 83 56 88 40 13 23 7 125 35 4.435 .225 .346 .923 .873 4.493 52 246 .525 .26 80 4590 9200 36 44 283 291 -50 227 199 28 .278 210 11 3.592 .427 -1.845 -1.227
19 6788 6181 158 172 6630 6009 6887 6606 164 177 6729 6434 0 0 2321 2144 51 84 100 100 100 100 12639 13163 1.103 .906 .956 .923 .934 1.501 80 360 .906 .95 100 4740 9210 36 46 297 307 0 7631 212 7419 1.119 8156 7943 .894 1.18 .162 .239
20 3552 2659 163 167 3389 2492 3581 2653 171 172 3418 2486 0 0 1146 655 50 70 100 100 100 100 5881 5904 1.36 .735 .727 .759 .71 1.389 52 289 .668 .92 90 4880 9210 36 45 311 320 0 3283 206 3077 .908 3275 3069 1.102 .898 -.14 -.155

Total number of rows: 43104

Table truncated, full table size 9674 Kbytes.




Supplementary data files not provided
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