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Sample GSM78095 Query DataSets for GSM78095
Status Public on Oct 15, 2005
Title MDA2B50r11a
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/2000-05/5949.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 3145 3602 306 98 2839 3504 null null 319 108 null null null null null null null null 100 100 null null null null .81 1.234 null null 1.306 null 80 400 1.061 .86 null null null 54 64 125 135 0 3035 83 2952 1.04 null null .962 null .056 null
2 2800 2830 310 101 2490 2729 null null 319 107 null null null null null null null null 100 100 null null null null .912 1.096 null null 1.136 null 80 331 .932 .84 null null null 54 64 140 150 0 2384 85 2299 .923 null null 1.083 null -.115 null
3 2141 1677 307 102 1834 1575 null null 313 106 null null null null null null null null 100 98 null null null null 1.164 .859 null null .914 null 80 410 .745 .85 null null null 53 64 154 165 0 1413 86 1327 .724 null null 1.382 null -.467 null
4 2280 1025 315 101 1965 924 null null 320 106 null null null null null null null null 99 92 null null null null 2.127 .47 null null .489 null 120 454 .432 .86 null null null 53 65 171 183 0 864 85 779 .396 null null 2.524 null -1.336 null
5 3147 993 315 101 2832 892 null null 327 108 null null null null null null null null 100 96 null null null null 3.175 .315 null null .341 null 80 353 .302 .87 null null null 52 63 185 196 0 837 85 752 .265 null null 3.768 null -1.914 null
6 2925 2871 335 99 2590 2772 null null 338 104 null null null null null null null null 100 97 null null null null .934 1.07 null null 1.123 null 80 404 .955 .85 null null null 53 64 200 211 0 2419 83 2336 .902 null null 1.109 null -.149 null
7 714 608 322 102 392 506 null null 332 104 null null null null null null null null 94 100 null null null null .775 1.291 null null 1.371 null 52 258 .726 .67 null null null 56 64 216 224 0 512 86 426 1.088 null null .919 null .121 null
8 615 379 319 113 296 266 null null 334 115 null null null null null null null null 93 100 null null null null 1.113 .899 null null .867 null 32 159 .577 .73 null null null 57 63 231 237 0 319 95 224 .757 null null 1.321 null -.401 null
9 2610 8892 331 113 2279 8779 null null 342 122 null null null null null null null null 96 100 null null null null .26 3.852 null null 3.704 null 80 425 3.152 .83 null null null 54 64 244 254 0 7492 95 7397 3.246 null null .308 null 1.698 null
10 761 633 319 124 442 509 null null 334 137 null null null null null null null null 93 100 null null null null .868 1.152 null null 1.087 null 32 215 .641 .63 null null null 54 61 261 268 0 533 104 429 .97 null null 1.031 null -.044 null
11 661 280 340 115 321 165 null null 347 123 null null null null null null null null 87 84 null null null null 1.945 .514 null null .491 null 32 209 .213 .43 null null null 55 62 274 281 0 236 97 139 .433 null null 2.309 null -1.207 null
12 990 1650 343 110 647 1540 null null 368 117 null null null null null null null null 81 98 null null null null .42 2.38 null null 2.305 null 80 368 1.187 .67 null null null 55 65 289 299 0 1390 93 1298 2.005 null null .499 null 1.004 null
13 5502 4541 341 113 5161 4428 null null 372 120 null null null null null null null null 98 100 null null null null 1.166 .858 null null .85 null 80 381 .7 .88 null null null 54 65 302 313 0 3826 95 3731 .723 null null 1.383 null -.468 null
14 10058 19401 332 114 9726 19287 null null 342 120 null null null null null null null null 100 100 null null null null .504 1.983 null null 1.942 null 80 423 1.582 .86 null null null 54 65 317 328 0 16346 96 16250 1.671 null null .599 null .741 null
15 869 639 312 110 557 529 null null 327 116 null null null null null null null null 97 100 null null null null 1.053 .95 null null .899 null 80 357 .678 .77 null null null 55 65 333 343 0 538 93 446 .8 null null 1.25 null -.322 null
16 944 787 325 113 619 674 null null 332 116 null null null null null null null null 97 100 null null null null .918 1.089 null null 1.06 null 80 360 .796 .8 null null null 55 65 348 358 0 663 95 568 .917 null null 1.09 null -.124 null
17 16637 17116 344 117 16293 16999 null null 357 122 null null null null null null null null 100 100 null null null null .958 1.043 null null 1.078 null 80 405 .934 .88 null null null 54 65 362 373 0 14421 99 14322 .879 null null 1.138 null -.186 null
18 486 245 358 118 128 127 null null 365 124 null null null null null null null null 33 38 null null null null 1.008 .992 null null .648 null 80 361 .464 .61 null null null 55 65 377 387 0 206 99 107 .836 null null 1.196 null -.258 null
19 4573 8358 369 115 4204 8243 null null 380 120 null null null null null null null null 95 100 null null null null .51 1.961 null null 1.89 null 80 367 1.597 .87 null null null 56 66 393 403 0 7042 97 6945 1.652 null null .605 null .724 null
20 3804 4878 376 108 3428 4770 null null 391 111 null null null null null null null null 100 100 null null null null .719 1.391 null null 1.451 null 80 344 1.18 .86 null null null 55 65 408 418 0 4110 91 4019 1.172 null null .853 null .229 null

Total number of rows: 24192

Table truncated, full table size 5811 Kbytes.




Supplementary data files not provided
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