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Sample GSM91639 Query DataSets for GSM91639
Status Public on Jan 11, 2006
Title GVNBPHF10_T8_C
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 GVNBPHF10_T8_C total RNA
Organism Homo sapiens
Characteristics GVNBPHF10_T8_C total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-12/35631.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 GPL3340
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
1 577 312 262 193 315 119 608 306 264 197 346 113 0 0 142 126 54 85 93 59 90 21 434 459 2.647 .378 .327 .317 .377 2.534 32 170 .4 .42 60 1880 8950 28 34 17 23 0 339 210 129 .411 333 123 2.435 .355 -1.284 -1.494
2 3198 669 254 201 2944 468 3112 688 253 212 2858 487 0 0 1186 240 49 81 100 93 100 93 3412 3345 6.291 .159 .17 .16 .157 1.46 32 176 .144 .82 60 2030 8950 28 34 32 38 0 727 218 509 .173 748 529 5.787 .185 -2.533 -2.433
3 1937 1227 246 197 1691 1030 1790 1237 250 204 1544 1040 0 0 993 596 58 107 100 100 100 91 2721 2584 1.642 .609 .674 .607 .626 1.539 12 98 .643 .92 50 2160 8940 27 32 45 50 0 1334 214 1120 .662 1345 1130 1.51 .732 -.595 -.45
4 1011 357 244 174 767 183 1180 347 254 194 936 173 0 0 342 119 55 87 100 83 100 50 950 1109 4.191 .239 .185 .29 .302 1.881 12 104 .131 .39 50 2310 8950 28 33 60 65 0 388 189 199 .259 377 188 3.856 .201 -1.947 -2.315
5 1458 2583 238 180 1220 2403 1363 2699 244 197 1125 2519 0 0 641 877 56 98 96 100 93 100 3623 3644 .508 1.97 2.239 2.323 2.126 2.084 32 230 1.943 .88 70 2460 8950 27 34 74 81 0 2808 196 2612 2.141 2934 2738 .467 2.434 1.098 1.283
6 789 306 241 191 548 115 829 295 243 198 588 104 0 0 139 75 56 93 100 58 100 8 663 692 4.765 .21 .177 .172 .208 2.42 12 98 .276 .54 50 2600 8940 27 32 89 94 0 333 208 125 .228 321 113 4.384 .192 -2.132 -2.379
7 1268 771 247 199 1021 572 1114 687 250 203 867 488 0 0 758 314 52 91 90 96 84 90 1593 1355 1.785 .56 .563 .636 .561 2.28 32 176 .464 .83 60 2750 8950 28 34 104 110 0 838 216 622 .609 747 530 1.642 .612 -.716 -.709
8 968 414 242 192 726 222 920 417 248 202 678 225 0 0 263 122 50 88 100 75 100 71 948 903 3.27 .306 .332 .276 .369 1.917 32 176 .29 .69 60 2900 8950 28 34 119 125 0 450 209 241 .332 453 245 3.009 .361 -1.589 -1.471
9 750 436 244 190 506 246 765 385 252 203 521 195 0 0 239 178 57 90 96 87 96 59 752 716 2.057 .486 .374 .542 .565 2.181 32 176 .466 .63 60 3050 8950 28 34 134 140 0 474 207 267 .528 418 212 1.892 .407 -.92 -1.298
10 606 285 254 209 352 76 621 268 258 222 367 59 0 0 105 127 57 82 100 41 100 25 428 426 4.632 .216 .161 .424 .442 2.285 12 68 .289 .36 40 3180 8950 29 33 148 152 0 310 227 83 .235 291 64 4.261 .175 -2.091 -2.517
11 1628 1107 234 192 1394 915 1776 1082 242 203 1542 890 0 0 798 467 53 86 94 100 90 98 2309 2432 1.523 .656 .577 .772 .679 2.266 52 309 .599 .91 80 3340 8960 28 36 162 170 0 1203 209 995 .713 1176 967 1.402 .627 -.487 -.673
12 2831 2703 230 195 2601 2508 1992 2088 233 201 1762 1893 0 0 2594 2254 52 90 88 96 84 92 5109 3655 1.037 .964 1.074 1.092 .987 2.324 52 274 .9 .94 80 3500 8950 27 35 178 186 0 2938 212 2726 1.048 2270 2058 .954 1.168 .068 .224
13 669 3099 236 197 433 2902 703 3240 239 202 467 3043 0 0 373 1307 48 88 75 100 73 100 3335 3510 .149 6.702 6.516 7.628 6.124 2.042 52 313 6.049 .87 90 3630 8950 26 35 190 199 0 3368 214 3154 7.285 3522 3308 .137 7.083 2.865 2.824
14 632 369 228 191 404 178 639 354 232 200 411 163 0 0 190 119 48 90 92 75 90 48 582 574 2.27 .441 .397 .48 .42 3.206 52 338 .406 .52 90 3780 8940 25 34 205 214 0 401 208 193 .479 385 177 2.088 .431 -1.062 -1.214
15 565 425 229 187 336 238 598 420 244 213 369 233 0 0 246 164 203 153 73 63 44 30 574 602 1.412 .708 .631 .604 .668 2.33 52 324 .613 .76 90 3930 8950 26 35 220 229 0 462 203 259 .77 457 253 1.299 .686 -.377 -.543
16 6766 8157 228 195 6538 7962 7217 8219 232 205 6989 8024 0 0 3679 3777 50 91 100 100 100 100 14500 15013 .821 1.218 1.148 1.385 1.206 1.617 52 302 1.16 .97 90 4080 8950 26 35 235 244 0 8866 212 8654 1.324 8934 8722 .755 1.248 .405 .32
17 1725 1414 229 203 1496 1211 1789 1207 231 204 1560 1004 0 0 1104 828 46 81 98 96 96 94 2707 2564 1.235 .809 .644 .868 .872 1.713 52 246 .764 .92 80 4220 8940 26 34 250 258 0 1537 221 1316 .88 1312 1091 1.137 .7 -.185 -.515
18 229 210 223 182 6 28 225 205 223 197 2 23 0 0 64 89 44 92 15 23 5 3 34 25 .214 4.667 11.5 2.305 2.317 5.29 52 255 11.035 .09 80 4360 8940 26 34 264 272 -50 228 198 30 5.072 223 25 .197 12.5 2.343 3.644
19 3733 3214 221 192 3512 3022 2494 2624 225 208 2273 2432 0 0 3058 2284 49 98 93 98 92 97 6534 4705 1.162 .86 1.07 1.19 .879 2.646 80 365 .789 .93 100 4510 8950 26 36 278 288 0 3493 209 3285 .935 2852 2643 1.069 1.163 -.096 .218
20 1831 1738 225 214 1606 1524 1865 1758 226 220 1640 1544 0 0 958 868 49 96 96 98 94 96 3130 3184 1.054 .949 .941 1.02 .922 2.247 52 289 .929 .91 90 4650 8940 25 34 292 301 0 1889 233 1657 1.031 1911 1678 .97 1.023 .045 .033

Total number of rows: 43104

Table truncated, full table size 9541 Kbytes.




Supplementary data files not provided
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