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Sample GSM91633 Query DataSets for GSM91633
Status Public on Jan 11, 2006
Title SKTZF16_T8_C1
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_C1 total RNA
Organism Homo sapiens
Characteristics SKTZF16_T8_C1 total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35540.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
1 813 418 178 140 635 278 813 383 182 146 635 243 0 0 265 155 51 61 98 94 98 84 913 878 2.284 .438 .383 .411 .442 1.912 52 245 .417 .79 80 1720 9170 33 41 32 40 0 492 165 327 .515 451 286 1.942 .45 -.957 -1.151
2 11542 7518 167 145 11375 7373 12670 7638 179 150 12503 7493 0 0 4341 2251 59 61 100 100 100 100 18748 19996 1.543 .648 .599 .691 .666 1.339 52 254 .605 .97 80 1860 9170 33 41 46 54 0 8845 171 8674 .763 8986 8815 1.311 .705 -.391 -.504
3 3179 2192 168 146 3011 2046 3344 1999 179 153 3176 1853 0 0 1615 912 57 67 100 100 96 100 5057 5029 1.472 .68 .583 .786 .676 1.817 32 210 .59 .94 70 2010 9170 33 40 61 68 0 2579 172 2407 .799 2352 2180 1.251 .686 -.323 -.543
4 2301 922 177 156 2124 766 2349 881 182 158 2172 725 0 0 819 267 53 63 100 100 100 100 2890 2897 2.773 .361 .334 .369 .359 1.448 32 212 .321 .91 70 2160 9160 32 39 76 83 0 1085 184 901 .424 1036 853 2.357 .393 -1.237 -1.349
5 3050 4785 187 151 2863 4634 3049 4885 197 160 2862 4734 0 0 1098 1260 66 64 100 100 100 100 7497 7596 .618 1.619 1.654 1.707 1.582 1.314 52 313 1.54 .96 90 2300 9170 32 41 89 98 0 5629 178 5452 1.904 5747 5569 .525 1.946 .929 .961
6 2202 951 182 157 2020 794 2395 957 203 163 2213 800 0 0 496 238 82 70 100 100 100 100 2814 3013 2.544 .393 .362 .392 .386 1.37 32 215 .379 .89 70 2450 9160 32 39 105 112 0 1119 185 934 .462 1126 941 2.162 .425 -1.113 -1.233
7 4221 2210 185 151 4036 2059 4416 2144 194 156 4231 1993 0 0 1575 727 58 59 100 100 100 100 6095 6224 1.96 .51 .471 .526 .529 1.41 52 265 .478 .94 80 2600 9170 33 41 120 128 0 2600 178 2422 .6 2522 2345 1.666 .554 -.737 -.852
8 1181 2330 184 155 997 2175 1153 2371 192 161 969 2216 0 0 440 739 53 60 100 100 100 100 3172 3185 .458 2.182 2.287 2.311 2.212 1.405 52 245 2.167 .94 80 2740 9170 33 41 134 142 0 2741 182 2559 2.567 2789 2607 .39 2.69 1.36 1.428
9 988 436 181 146 807 290 975 443 187 154 794 297 0 0 312 165 52 61 100 88 100 82 1097 1091 2.783 .359 .374 .334 .381 1.689 80 366 .349 .83 100 2890 9170 32 42 148 158 0 513 172 341 .423 521 349 2.365 .44 -1.242 -1.184
10 872 274 181 154 691 120 888 282 194 160 707 128 0 0 258 105 88 66 100 78 96 43 811 835 5.758 .174 .181 .176 .192 2.183 32 148 .161 .57 60 3040 9160 33 39 165 171 0 322 181 141 .204 332 151 4.895 .213 -2.291 -2.231
11 2437 7788 182 152 2255 7636 2579 8240 193 159 2397 8088 0 0 982 2658 72 60 97 100 97 100 9891 10485 .295 3.386 3.374 3.753 3.472 1.562 80 356 3.313 .97 100 3180 9170 32 42 177 187 0 9162 179 8984 3.984 9694 9515 .251 3.97 1.994 1.989
12 8596 10794 179 140 8417 10654 9403 11048 212 173 9224 10908 0 0 5258 5790 181 136 96 100 94 100 19071 20132 .79 1.266 1.183 1.512 1.329 1.655 52 238 1.182 .97 80 3320 9160 32 40 192 200 0 12699 165 12534 1.489 12998 12833 .672 1.391 .574 .476
13 2096 8621 185 155 1911 8466 2214 8565 210 173 2029 8410 0 0 652 2067 150 111 100 100 98 100 10377 10439 .226 4.43 4.145 4.658 4.224 1.321 80 412 4.384 .96 110 3470 9170 31 42 205 216 0 10142 182 9960 5.212 10076 9894 .192 4.876 2.382 2.286
14 693 303 192 149 501 154 680 292 201 159 488 143 0 0 156 86 77 66 100 90 100 55 655 631 3.253 .307 .293 .288 .277 1.896 52 290 .264 .6 90 3620 9170 32 41 221 230 0 356 175 181 .362 344 168 2.765 .345 -1.467 -1.536
15 895 531 193 156 702 375 907 516 199 164 714 360 0 0 233 185 57 62 98 97 97 93 1077 1074 1.872 .534 .504 .498 .483 1.759 80 320 .521 .83 100 3770 9170 32 42 236 246 0 625 184 441 .628 607 424 1.591 .593 -.67 -.753
16 9625 10639 194 159 9431 10480 10101 11270 201 165 9907 11111 0 0 3724 3451 58 58 100 100 100 100 19911 21018 .9 1.111 1.122 1.156 1.112 1.315 80 353 1.073 .97 100 3910 9170 32 42 250 260 0 12516 187 12329 1.307 13259 13072 .765 1.319 .387 .4
17 5383 6575 182 149 5201 6426 5555 6612 190 156 5373 6463 0 0 1269 1571 57 61 100 100 100 100 11627 11836 .809 1.236 1.203 1.244 1.231 1.309 52 252 1.234 .97 80 4060 9170 33 41 266 274 0 7735 175 7560 1.454 7779 7604 .688 1.415 .54 .501
18 310 227 178 151 132 76 201 184 191 161 23 33 0 0 280 167 71 60 30 40 19 23 208 56 1.737 .576 1.435 1.23 .903 4.069 52 231 .585 .77 80 4220 9160 32 40 282 290 -50 267 178 89 .677 216 39 1.476 1.688 -.562 .755
19 7303 8420 179 155 7124 8265 7964 9048 187 174 7785 8893 0 0 2657 2486 60 254 100 100 98 100 15389 16678 .862 1.16 1.142 1.287 1.172 1.677 80 320 1.114 .97 100 4350 9170 32 42 294 304 0 9906 182 9724 1.365 10645 10462 .733 1.344 .449 .426
20 3322 2453 181 150 3141 2303 3156 2404 234 183 2975 2254 0 0 1277 820 291 187 100 100 98 100 5444 5229 1.364 .733 .758 .745 .746 1.338 52 301 .671 .96 90 4490 9160 31 40 308 317 0 2886 176 2709 .863 2828 2652 1.159 .891 -.213 -.166

Total number of rows: 43104

Table truncated, full table size 9682 Kbytes.




Supplementary data files not provided
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