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Sample GSM78102 Query DataSets for GSM78102
Status Public on Oct 15, 2005
Title 32 hrs R1881
Sample type RNA
 
Channel 1
Source name CR
Organism Homo sapiens
Characteristics CR
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 32 hrs 1 nM R1881
Organism Homo sapiens
Characteristics 32 hrs 1 nM R1881
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, androgen
Image: http://smd.stanford.edu/MicroArray/gifs/2000-06/6983.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 3353 2463 126 98 3227 2365 null null 136 111 null null null null null null null null 100 100 null null null null 1.364 .733 null null .727 null 80 462 .735 .97 null null null 54 65 117 128 0 2831 112 2719 .843 null null 1.187 null -.247 null
2 1692 1897 123 95 1569 1802 null null 132 106 null null null null null null null null 100 100 null null null null .871 1.149 null null 1.165 null 80 336 1.067 .94 null null null 56 66 132 142 0 2180 109 2071 1.32 null null .758 null .4 null
3 1378 1799 117 97 1261 1702 null null 126 111 null null null null null null null null 100 100 null null null null .741 1.35 null null 1.356 null 80 401 1.25 .95 null null null 56 67 147 158 0 2067 111 1956 1.551 null null .645 null .633 null
4 1408 321 119 103 1289 218 null null 136 123 null null null null null null null null 100 80 null null null null 5.913 .169 null null .153 null 80 384 .141 .46 null null null 55 66 162 173 0 368 118 250 .194 null null 5.156 null -2.366 null
5 5472 2335 113 99 5359 2236 null null 128 118 null null null null null null null null 99 100 null null null null 2.397 .417 null null .42 null 120 451 .395 .97 null null null 55 67 177 189 0 2683 113 2570 .48 null null 2.085 null -1.06 null
6 1379 1986 116 97 1263 1889 null null 125 107 null null null null null null null null 100 100 null null null null .669 1.496 null null 1.512 null 80 365 1.387 .94 null null null 57 67 193 203 0 2282 111 2171 1.719 null null .582 null .782 null
7 665 448 123 97 542 351 null null 131 109 null null null null null null null null 100 96 null null null null 1.544 .648 null null .651 null 52 312 .563 .85 null null null 57 66 209 218 0 514 111 403 .744 null null 1.345 null -.428 null
8 929 387 124 99 805 288 null null 129 114 null null null null null null null null 100 92 null null null null 2.795 .358 null null .271 null 52 256 .264 .42 null null null 58 66 224 232 0 444 113 331 .411 null null 2.432 null -1.282 null
9 13235 2528 116 101 13119 2427 null null 125 114 null null null null null null null null 100 100 null null null null 5.405 .185 null null .195 null 80 382 .178 .96 null null null 57 67 239 249 0 2905 116 2789 .213 null null 4.704 null -2.234 null
10 846 526 124 97 722 429 null null 131 110 null null null null null null null null 100 98 null null null null 1.683 .594 null null .574 null 52 310 .534 .84 null null null 57 66 253 262 0 604 111 493 .683 null null 1.465 null -.55 null
11 1216 209 118 99 1098 110 null null 124 106 null null null null null null null null 100 76 null null null null 9.982 .1 null null .109 null 52 311 .089 .68 null null null 58 67 269 278 0 240 113 127 .116 null null 8.646 null -3.112 null
12 5469 385 124 110 5345 275 null null 133 118 null null null null null null null null 100 100 null null null null 19.436 .051 null null .052 null 52 244 .047 .86 null null null 59 67 283 291 0 442 126 316 .059 null null 16.915 null -4.08 null
13 3006 4592 133 125 2873 4467 null null 148 196 null null null null null null null null 100 100 null null null null .643 1.555 null null 1.521 null 80 359 1.488 .97 null null null 59 69 298 308 0 5278 143 5135 1.787 null null .559 null .838 null
14 22266 15589 143 127 22123 15462 null null 159 197 null null null null null null null null 100 100 null null null null 1.431 .699 null null .707 null 80 436 .688 .98 null null null 58 69 311 322 0 17918 145 17773 .803 null null 1.245 null -.316 null
15 1865 491 137 119 1728 372 null null 148 142 null null null null null null null null 100 93 null null null null 4.645 .215 null null .228 null 80 349 .196 .87 null null null 59 69 328 338 0 564 136 428 .248 null null 4.037 null -2.013 null
16 2413 922 132 123 2281 799 null null 136 143 null null null null null null null null 100 97 null null null null 2.855 .35 null null .277 null 80 339 .356 .55 null null null 59 69 342 352 0 1059 141 918 .402 null null 2.485 null -1.313 null
17 9643 16527 134 136 9509 16391 null null 141 159 null null null null null null null null 100 100 null null null null .58 1.724 null null 1.726 null 80 390 1.674 .98 null null null 59 70 356 367 0 18996 156 18840 1.981 null null .505 null .986 null
18 219 226 137 135 82 91 null null 145 156 null null null null null null null null 30 31 null null null null .901 1.11 null null 1.133 null 80 383 .455 .5 null null null 59 69 371 381 0 259 155 104 1.268 null null .788 null .343 null
19 5375 6048 140 143 5235 5905 null null 147 163 null null null null null null null null 100 100 null null null null .887 1.128 null null 1.126 null 52 313 1.079 .97 null null null 60 69 386 395 0 6951 164 6787 1.296 null null .771 null .375 null
20 1732 952 130 133 1602 819 null null 141 153 null null null null null null null null 100 100 null null null null 1.956 .511 null null .511 null 52 334 .479 .51 null null null 60 69 401 410 0 1094 152 942 .588 null null 1.701 null -.766 null

Total number of rows: 24192

Table truncated, full table size 5799 Kbytes.




Supplementary data files not provided
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