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Sample GSM91648 Query DataSets for GSM91648
Status Public on Jan 11, 2006
Title SKTZF16_T8_T2
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_T8_T2 total RNA
Organism Homo sapiens
Characteristics SKTZF16_T8_T2 total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35547.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
1 852 556 139 139 713 417 803 548 321 147 664 409 0 0 269 207 2462 58 0 96 0 93 1130 1073 1.71 .585 .616 .541 .584 1.694 32 205 .003 .04 70 2220 9170 17 24 38 45 0 678 170 509 .713 668 499 1.402 .751 -.488 -.413
2 12075 15977 137 142 11938 15835 13404 17940 277 151 13267 17798 0 0 6626 8094 2116 69 86 100 75 100 27773 31065 .754 1.326 1.342 1.576 1.344 1.929 52 278 1.288 .98 80 2370 9170 17 25 53 61 0 19484 173 19311 1.618 21878 21705 .618 1.636 .694 .71
3 3771 2159 142 139 3629 2020 4104 2113 148 149 3962 1974 0 0 1782 950 42 67 96 100 96 96 5649 5936 1.797 .557 .498 .572 .576 1.744 32 214 .528 .93 70 2510 9160 16 23 67 74 0 2633 170 2463 .679 2577 2407 1.473 .608 -.559 -.719
4 2627 925 139 149 2488 776 2901 919 150 152 2762 770 0 0 1141 381 55 63 100 96 100 96 3264 3532 3.206 .312 .279 .306 .29 1.45 32 212 .278 .89 70 2660 9160 16 23 82 89 0 1128 182 946 .38 1121 939 2.629 .34 -1.395 -1.556
5 3221 3945 151 134 3070 3811 3390 4110 162 141 3239 3976 0 0 1358 1679 79 56 100 100 100 100 6881 7215 .806 1.241 1.228 1.276 1.239 1.524 52 278 1.246 .95 80 2810 9160 16 24 97 105 0 4811 163 4648 1.514 5012 4849 .661 1.497 .598 .582
6 2184 862 144 139 2040 723 2362 911 156 146 2218 772 0 0 796 306 82 57 100 100 100 100 2763 2990 2.822 .354 .348 .351 .324 1.548 32 209 .316 .88 70 2950 9160 16 23 111 118 0 1051 170 882 .432 1111 941 2.314 .424 -1.21 -1.236
7 5276 2552 143 146 5133 2406 6352 3059 151 153 6209 2913 0 0 2828 1210 47 60 100 100 100 100 7539 9122 2.133 .469 .469 .535 .49 1.755 52 266 .444 .96 80 3100 9170 17 25 126 134 0 3112 178 2934 .572 3730 3552 1.749 .572 -.807 -.806
8 1274 2663 143 134 1131 2529 1329 2756 150 140 1186 2622 0 0 577 1175 48 54 98 100 96 100 3660 3808 .447 2.236 2.211 2.476 2.198 1.767 52 278 2.257 .95 80 3240 9170 17 25 140 148 0 3248 163 3084 2.727 3361 3198 .367 2.696 1.447 1.431
9 1173 635 141 145 1032 490 1174 631 165 150 1033 486 0 0 290 183 372 58 100 100 86 96 1522 1519 2.106 .475 .47 .456 .482 1.509 52 327 .443 .85 90 3400 9170 16 25 155 164 0 774 177 598 .579 770 593 1.727 .574 -.788 -.802
10 710 604 144 152 566 452 680 623 149 156 536 471 0 0 273 237 47 58 100 96 96 90 1018 1007 1.252 .799 .879 .74 .78 1.859 32 202 .772 .84 70 3540 9160 16 23 170 177 0 737 185 551 .974 760 574 1.027 1.072 -.038 .1
11 4630 5928 142 150 4488 5778 4637 5538 166 153 4495 5388 0 0 1222 1603 177 60 100 100 100 100 10266 9883 .777 1.287 1.199 1.313 1.269 1.397 52 266 1.283 .95 80 3690 9170 17 25 185 193 0 7229 183 7046 1.57 6754 6571 .637 1.462 .651 .548
12 10532 9552 144 154 10388 9398 9768 9300 150 155 9624 9146 0 0 8199 7541 45 61 96 98 96 98 19786 18770 1.105 .905 .95 1.08 .928 2.383 52 243 .908 .96 80 3820 9170 17 25 198 206 0 11649 188 11461 1.103 11341 11154 .906 1.159 .142 .213
13 2842 11629 147 160 2695 11469 2927 11862 154 174 2780 11702 0 0 671 2724 53 82 100 100 100 100 14164 14482 .235 4.256 4.209 4.298 4.337 1.383 52 324 4.371 .96 90 3970 9170 16 25 212 221 0 14182 195 13987 5.19 14466 14271 .193 5.133 2.376 2.36
14 804 616 149 159 655 457 789 618 161 170 640 459 0 0 186 195 71 83 100 98 100 96 1112 1099 1.433 .698 .717 .687 .653 1.542 52 334 .688 .83 90 4130 9170 16 25 228 237 0 751 194 557 .851 754 560 1.175 .875 -.233 -.193
15 897 554 141 160 756 394 930 584 155 169 789 424 0 0 238 164 67 69 100 94 100 94 1150 1213 1.919 .521 .537 .486 .51 1.705 52 242 .515 .87 80 4280 9170 17 25 244 252 0 676 195 480 .636 712 517 1.573 .655 -.654 -.61
16 16398 18744 143 157 16255 18587 18952 20094 154 173 18809 19937 0 0 7216 8015 66 101 100 100 98 100 34842 38746 .875 1.143 1.06 1.239 1.149 1.856 52 302 1.113 .97 90 4410 9170 16 25 256 265 0 22859 191 22667 1.394 24505 24313 .717 1.293 .48 .37
17 4844 12850 143 159 4701 12691 5435 13627 196 179 5292 13468 0 0 2210 6247 519 140 94 100 88 100 17392 18760 .37 2.7 2.545 2.66 2.684 1.392 52 265 2.754 .98 80 4560 9170 17 25 272 280 0 15671 194 15477 3.292 16618 16424 .304 3.104 1.719 1.634
18 306 432 138 158 168 274 149 196 144 163 11 38 0 0 473 693 45 58 25 38 15 23 442 49 .613 1.631 3.455 2.473 2.3 5.608 52 254 1.594 .83 80 4720 9170 17 25 288 296 -50 527 193 334 1.989 239 46 .503 4.213 .992 2.075
19 9144 9460 134 160 9010 9300 9765 9971 145 166 9631 9811 0 0 2828 2723 83 60 100 100 100 100 18310 19442 .969 1.032 1.019 1.052 1.033 1.366 52 292 1.015 .98 90 4860 9170 16 25 301 310 0 11537 195 11341 1.259 12160 11965 .794 1.242 .332 .313
20 4355 2732 130 150 4225 2582 4454 2549 137 158 4324 2399 0 0 1317 869 38 59 100 100 100 100 6807 6723 1.636 .611 .555 .616 .606 1.386 52 309 .598 .95 90 5010 9170 16 25 316 325 0 3332 183 3149 .745 3109 2926 1.342 .677 -.424 -.564

Total number of rows: 43104

Table truncated, full table size 9705 Kbytes.




Supplementary data files not provided
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