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Sample GSM91647 Query DataSets for GSM91647
Status Public on Jan 11, 2006
Title SKTZF16_T2_C1
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_C1 total RNA
Organism Homo sapiens
Characteristics SKTZF16_T2_C1 total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35538.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
1 799 425 144 134 655 291 760 434 153 148 616 300 0 0 242 128 51 61 100 90 100 90 946 916 2.251 .444 .487 .399 .431 2.3 32 189 .386 .77 70 1600 9270 43 50 24 31 0 447 141 306 .468 457 316 2.138 .513 -1.096 -.964
2 8488 6584 152 146 8336 6438 9645 7071 160 147 9493 6925 0 0 3886 2469 55 58 100 100 100 100 14774 16418 1.295 .772 .729 .842 .757 1.543 52 254 .719 .97 80 1740 9270 43 51 38 46 0 6931 154 6777 .813 7443 7289 1.23 .768 -.299 -.381
3 2208 1770 153 143 2055 1627 2073 1748 161 146 1920 1605 0 0 1398 791 54 57 100 100 100 100 3682 3525 1.263 .792 .836 .956 .847 1.728 32 220 .689 .93 70 1890 9260 42 49 53 60 0 1863 151 1713 .833 1840 1689 1.2 .88 -.263 -.185
4 1768 787 155 145 1613 642 1780 724 159 148 1625 579 0 0 655 202 41 51 100 100 100 100 2255 2204 2.512 .398 .356 .412 .386 1.381 32 204 .354 .9 70 2040 9260 42 49 68 75 0 828 153 676 .419 762 609 2.387 .375 -1.255 -1.415
5 2284 3916 157 154 2127 3762 2390 3729 163 155 2233 3575 0 0 875 1414 47 64 100 100 100 100 5889 5808 .565 1.769 1.601 1.851 1.797 1.395 52 323 1.79 .96 90 2180 9260 41 50 81 90 0 4122 162 3960 1.862 3925 3763 .537 1.685 .897 .753
6 1478 575 159 149 1319 426 1553 605 166 155 1394 456 0 0 460 191 48 65 100 98 100 94 1745 1850 3.096 .323 .327 .306 .327 1.556 52 251 .313 .89 80 2340 9260 42 50 98 106 0 605 157 448 .34 637 480 2.941 .344 -1.557 -1.538
7 3444 2081 158 148 3286 1933 3433 2076 165 152 3275 1928 0 0 937 494 44 58 100 100 100 100 5219 5203 1.7 .588 .589 .594 .605 1.211 52 285 .567 .97 90 2480 9260 41 50 111 120 0 2191 156 2035 .619 2185 2029 1.615 .62 -.691 -.69
8 955 1529 156 140 799 1389 950 1459 163 150 794 1319 0 0 261 340 46 58 100 100 100 100 2188 2113 .575 1.738 1.661 1.799 1.729 1.35 52 245 1.765 .93 80 2620 9260 42 50 126 134 0 1609 147 1462 1.83 1536 1388 .546 1.749 .872 .806
9 924 490 161 154 763 336 914 462 168 162 753 308 0 0 279 178 52 65 98 98 98 86 1099 1061 2.271 .44 .409 .409 .433 1.809 80 368 .433 .81 100 2770 9260 41 51 140 150 0 516 162 354 .464 486 324 2.157 .431 -1.109 -1.216
10 802 300 158 165 644 135 804 296 163 170 646 131 0 0 154 95 47 70 100 75 100 43 779 777 4.77 .21 .203 .161 .196 2.774 32 154 .191 .57 60 2920 9250 42 48 157 163 0 316 174 142 .221 312 138 4.532 .213 -2.18 -2.228
11 2281 8220 154 162 2127 8058 2324 8446 169 198 2170 8284 0 0 735 2079 87 221 100 100 100 100 10185 10454 .264 3.788 3.818 3.932 3.793 1.233 52 314 3.645 .98 90 3050 9260 41 50 168 177 0 8653 171 8482 3.988 8891 8720 .251 4.018 1.996 2.007
12 8228 14064 162 171 8066 13893 7436 15769 390 482 7274 15598 0 0 4201 5400 1098 1386 90 96 90 93 21959 22872 .581 1.722 2.144 1.914 1.604 1.576 32 222 1.616 .93 70 3200 9250 41 48 184 191 0 14804 180 14624 1.813 16599 16419 .552 2.257 .858 1.175
13 1732 7878 166 160 1566 7718 1756 7991 298 329 1590 7831 0 0 399 1651 852 1070 95 100 36 98 9284 9421 .203 4.928 4.925 4.97 4.8 1.265 80 372 5.083 .94 100 3360 9260 41 51 199 209 0 8293 168 8124 5.188 8412 8243 .193 5.184 2.375 2.374
14 604 312 161 151 443 161 593 320 175 156 432 169 0 0 169 94 69 63 100 80 98 65 604 601 2.752 .363 .391 .334 .373 2.086 80 309 .337 .66 100 3500 9260 41 51 213 223 0 328 159 169 .383 337 178 2.614 .412 -1.386 -1.28
15 924 583 162 157 762 426 930 570 169 163 768 413 0 0 231 189 47 61 100 98 100 98 1188 1181 1.789 .559 .538 .54 .542 1.441 80 304 .583 .89 100 3650 9260 41 51 228 238 0 614 165 448 .588 600 435 1.699 .566 -.765 -.821
16 9689 14763 162 164 9527 14599 9895 15359 174 172 9733 15195 0 0 4221 5740 59 77 100 100 100 100 24126 24928 .653 1.532 1.561 1.598 1.568 1.433 80 366 1.512 .96 100 3790 9260 41 51 242 252 0 15540 173 15367 1.613 16167 15995 .62 1.643 .69 .717
17 4138 6149 153 159 3985 5990 4433 6279 168 172 4280 6120 0 0 1300 2055 63 85 100 100 100 100 9975 10400 .665 1.503 1.43 1.477 1.52 1.289 52 290 1.521 .97 90 3950 9260 41 50 258 267 0 6473 167 6305 1.582 6609 6442 .632 1.505 .662 .59
18 253 184 150 148 103 36 191 164 157 158 41 16 0 0 190 102 40 63 50 26 32 11 139 57 2.861 .35 .39 .525 .478 3.96 52 236 .395 .49 80 4090 9240 40 48 273 281 -50 194 156 38 .368 173 17 2.718 .411 -1.443 -1.284
19 6634 7754 158 147 6476 7607 7054 8565 167 162 6896 8418 0 0 2074 2518 50 107 100 100 100 100 14083 15314 .851 1.175 1.221 1.178 1.178 1.389 80 361 1.173 .98 100 4230 9250 40 50 286 296 0 8162 155 8007 1.236 9016 8861 .809 1.285 .306 .362
20 3518 3382 167 155 3351 3227 3688 3428 175 166 3521 3273 0 0 1065 897 68 75 100 100 100 100 6578 6794 1.038 .963 .93 .988 .932 1.281 52 300 .908 .96 90 4380 9250 40 49 301 310 0 3560 163 3397 1.014 3608 3445 .987 .978 .02 -.031

Total number of rows: 43104

Table truncated, full table size 9683 Kbytes.




Supplementary data files not provided
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