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Sample GSM78092 Query DataSets for GSM78092
Status Public on Oct 15, 2005
Title MDA2A48r11a
Sample type RNA
 
Channel 1
Source name ethanol control
Organism Homo sapiens
Characteristics ethanol control
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 1 nM R1881
Organism Homo sapiens
Characteristics 1 nM R1881
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5890.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Oct 14, 2005
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 GPL2948
Series (1)
GSE3451 Transcriptional programs activated by exposure of human prostate cancer cells to androgen.

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 LOG_RAT2N_MEDIANs 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 LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN 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 LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN 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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 2330 3478 140 77 2190 3401 null null 161 93 null null null null null null null null 100 100 null null null null .644 1.553 null null 1.568 null 80 464 1.402 .93 null null null 38 49 89 100 0 3548 78 3470 1.584 null null .631 null .664 null
2 2207 2214 146 77 2061 2137 null null 167 95 null null null null null null null null 100 100 null null null null .964 1.037 null null 1.076 null 80 390 .955 .92 null null null 38 49 105 116 0 2259 78 2181 1.058 null null .945 null .082 null
3 1466 1491 137 71 1329 1420 null null 147 75 null null null null null null null null 100 100 null null null null .936 1.068 null null 1.064 null 80 405 .977 .91 null null null 38 49 121 132 0 1521 72 1449 1.09 null null .917 null .125 null
4 740 227 151 72 589 155 null null 162 84 null null null null null null null null 100 90 null null null null 3.8 .263 null null .257 null 80 374 .225 .74 null null null 37 48 136 147 0 231 73 158 .268 null null 3.728 null -1.898 null
5 5010 2217 147 76 4863 2141 null null 159 90 null null null null null null null null 100 98 null null null null 2.271 .44 null null .452 null 120 520 .413 .94 null null null 36 49 149 162 0 2262 77 2185 .449 null null 2.226 null -1.154 null
6 1392 1425 133 72 1259 1353 null null 143 81 null null null null null null null null 100 100 null null null null .931 1.075 null null 1.087 null 80 407 .926 .92 null null null 38 49 165 176 0 1454 73 1381 1.097 null null .912 null .133 null
7 455 268 124 72 331 196 null null 134 76 null null null null null null null null 100 98 null null null null 1.689 .592 null null .605 null 52 323 .421 .73 null null null 38 47 181 190 0 273 73 200 .604 null null 1.655 null -.727 null
8 375 146 136 82 239 64 null null 162 102 null null null null null null null null 69 0 null null null null 3.734 .268 null null .278 null 52 313 .239 .21 null null null 38 47 196 205 0 148 83 65 .272 null null 3.677 null -1.879 null
9 1476 3782 136 75 1340 3707 null null 145 84 null null null null null null null null 98 100 null null null null .361 2.766 null null 2.78 null 80 420 2.264 .9 null null null 38 49 210 221 0 3859 76 3783 2.823 null null .354 null 1.497 null
10 528 345 129 73 399 272 null null 139 78 null null null null null null null null 96 100 null null null null 1.467 .682 null null .678 null 52 264 .547 .82 null null null 39 47 228 236 0 352 74 278 .697 null null 1.435 null -.521 null
11 447 213 130 75 317 138 null null 139 82 null null null null null null null null 98 90 null null null null 2.297 .435 null null .41 null 52 288 .287 .61 null null null 38 47 241 250 0 217 76 141 .445 null null 2.248 null -1.169 null
12 1108 1213 138 74 970 1139 null null 148 80 null null null null null null null null 100 100 null null null null .852 1.174 null null 1.166 null 52 301 1.092 .89 null null null 38 47 255 264 0 1237 75 1162 1.198 null null .835 null .261 null
13 3706 3154 144 79 3562 3075 null null 154 84 null null null null null null null null 100 100 null null null null 1.158 .863 null null .85 null 80 418 .806 .94 null null null 38 49 269 280 0 3218 80 3138 .881 null null 1.135 null -.183 null
14 6280 10080 140 82 6140 9998 null null 150 87 null null null null null null null null 100 100 null null null null .614 1.628 null null 1.727 null 120 564 1.599 .94 null null null 36 49 284 297 0 10285 83 10202 1.662 null null .602 null .733 null
15 726 486 149 79 577 407 null null 158 84 null null null null null null null null 100 97 null null null null 1.418 .705 null null .74 null 80 321 .585 .81 null null null 38 48 301 311 0 495 80 415 .719 null null 1.39 null -.475 null
16 882 748 153 82 729 666 null null 163 87 null null null null null null null null 100 98 null null null null 1.095 .914 null null .93 null 80 347 .79 .88 null null null 38 48 315 325 0 763 83 680 .933 null null 1.072 null -.1 null
17 11892 15034 140 79 11752 14955 null null 163 85 null null null null null null null null 100 100 null null null null .786 1.273 null null 1.255 null 80 388 1.127 .92 null null null 38 49 329 340 0 15340 80 15260 1.299 null null .77 null .377 null
18 197 120 133 77 64 43 null null 160 82 null null null null null null null null 10 32 null null null null 1.488 .672 null null .569 null 80 361 .32 .58 null null null 38 48 345 355 0 122 78 44 .688 null null 1.455 null -.541 null
19 3257 4802 131 77 3126 4725 null null 143 83 null null null null null null null null 100 100 null null null null .662 1.512 null null 1.48 null 80 346 1.363 .88 null null null 38 48 360 370 0 4900 78 4822 1.543 null null .648 null .625 null
20 2017 1940 135 76 1882 1864 null null 143 82 null null null null null null null null 97 98 null null null null 1.01 .99 null null .991 null 80 363 .869 .93 null null null 39 49 375 385 0 1979 77 1902 1.011 null null .989 null .015 null

Total number of rows: 24192

Table truncated, full table size 5689 Kbytes.




Supplementary data files not provided
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