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Sample GSM91649 Query DataSets for GSM91649
Status Public on Jan 11, 2006
Title SKTZF16_T2_T1
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_T2_T1 total RNA
Organism Homo sapiens
Characteristics SKTZF16_T2_T1 total RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: prostate cancer, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35539.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
1 915 435 191 152 724 283 938 392 203 159 747 240 0 0 156 154 86 66 100 100 100 87 1007 987 2.558 .391 .321 .348 .336 1.662 32 196 .399 .8 70 1660 9250 41 48 22 29 0 506 177 329 .455 456 279 2.2 .374 -1.138 -1.42
2 12206 9323 183 152 12023 9171 12650 9352 187 157 12467 9200 0 0 3209 2229 50 61 100 100 100 100 21194 21667 1.311 .763 .738 .779 .766 1.375 52 320 .737 .97 90 1790 9240 39 48 34 43 0 10841 177 10664 .887 10874 10698 1.127 .858 -.173 -.221
3 3338 2515 187 151 3151 2364 3426 2529 197 155 3239 2378 0 0 1622 986 69 61 100 100 96 100 5515 5617 1.333 .75 .734 .83 .725 1.926 32 222 .683 .95 70 1940 9230 39 46 50 57 0 2924 176 2749 .872 2941 2765 1.146 .854 -.197 -.228
4 2174 936 190 152 1984 784 2213 926 203 158 2023 774 0 0 694 241 78 59 100 100 100 100 2768 2797 2.531 .395 .383 .405 .435 1.485 32 208 .358 .9 70 2080 9230 39 46 64 71 0 1088 177 912 .459 1077 900 2.176 .445 -1.122 -1.168
5 2939 6044 198 153 2741 5891 3007 5977 204 165 2809 5824 0 0 930 1636 74 116 100 100 100 100 8632 8633 .465 2.149 2.073 2.19 2.111 1.318 52 300 2.078 .95 90 2220 9240 39 48 77 86 0 7028 178 6850 2.499 6950 6772 .4 2.411 1.321 1.27
6 1922 878 196 146 1726 732 2001 905 204 167 1805 759 0 0 714 329 72 125 100 96 100 94 2458 2564 2.358 .424 .42 .418 .415 1.556 52 265 .408 .92 80 2370 9240 40 48 93 101 0 1021 170 851 .493 1052 883 2.028 .489 -1.02 -1.032
7 3992 2042 197 141 3795 1901 4172 2084 203 147 3975 1943 0 0 1591 598 54 54 100 100 100 100 5696 5918 1.996 .501 .489 .535 .483 1.47 52 264 .462 .96 80 2520 9240 40 48 108 116 0 2374 164 2210 .582 2423 2259 1.717 .568 -.78 -.815
8 1365 2839 195 151 1170 2688 1313 2868 209 153 1118 2717 0 0 449 688 68 52 100 100 100 100 3858 3835 .435 2.297 2.43 2.408 2.502 1.428 52 242 2.259 .93 80 2670 9240 40 48 123 131 0 3301 176 3126 2.671 3335 3159 .374 2.826 1.418 1.499
9 1280 566 184 156 1096 410 1297 569 196 158 1113 413 0 0 335 179 68 56 100 97 100 92 1506 1526 2.673 .374 .371 .344 .37 1.737 80 356 .361 .87 100 2810 9240 39 49 136 146 0 658 181 477 .435 662 480 2.299 .431 -1.201 -1.213
10 979 330 173 138 806 192 1008 302 178 151 835 164 0 0 261 129 48 62 100 93 100 62 998 999 4.198 .238 .196 .206 .179 2.119 32 192 .188 .58 70 2960 9230 39 46 152 159 0 384 160 223 .277 351 191 3.61 .228 -1.852 -2.13
11 2950 9768 177 151 2773 9617 2899 10134 205 262 2722 9983 0 0 855 2405 162 778 100 100 100 100 12390 12705 .288 3.468 3.668 3.526 3.507 1.314 52 305 3.48 .96 90 3090 9240 39 48 164 173 0 11358 176 11183 4.033 11784 11608 .248 4.265 2.012 2.092
12 11732 17019 188 184 11544 16835 11873 18406 636 1009 11685 18222 0 0 5931 7439 1830 3024 93 90 87 90 28379 29907 .686 1.458 1.559 1.606 1.434 1.623 32 222 1.428 .96 70 3230 9230 39 46 179 186 0 19790 214 19576 1.696 21402 21188 .59 1.813 .762 .859
13 2470 10665 187 177 2283 10488 2427 10205 416 554 2240 10028 0 0 738 2909 1368 2188 91 100 28 100 12771 12268 .218 4.594 4.477 4.687 4.543 1.257 80 405 4.662 .96 100 3400 9240 39 49 195 205 0 12401 206 12195 5.342 11866 11660 .187 5.206 2.417 2.38
14 1360 593 180 153 1180 440 1038 358 189 165 858 205 0 0 1984 1086 60 66 100 96 100 69 1620 1063 2.682 .373 .239 .256 .282 2.118 52 289 .479 .9 90 3550 9230 38 47 210 219 0 690 178 512 .434 416 238 2.306 .278 -1.206 -1.848
15 1031 572 187 150 844 422 1056 565 196 160 869 415 0 0 239 168 55 60 100 100 98 95 1266 1284 2 .5 .478 .483 .48 1.553 80 309 .495 .88 100 3690 9240 39 49 224 234 0 665 174 491 .581 657 483 1.72 .555 -.782 -.849
16 14641 18377 182 154 14459 18223 14762 18828 190 161 14580 18674 0 0 5202 6106 53 58 100 100 100 100 32682 33254 .793 1.26 1.281 1.301 1.237 1.394 80 327 1.254 .97 100 3830 9240 39 49 238 248 0 21369 179 21190 1.465 21893 21714 .682 1.489 .551 .575
17 6168 9162 182 149 5986 9013 6281 9257 193 158 6099 9108 0 0 1710 2766 58 61 100 100 100 100 14999 15207 .664 1.506 1.493 1.49 1.524 1.198 52 299 1.514 .97 90 3980 9240 39 48 253 262 0 10653 173 10480 1.751 10764 10591 .571 1.736 .808 .796
18 268 189 183 159 85 30 203 177 191 167 20 18 0 0 182 99 49 67 34 19 21 9 115 38 2.833 .353 .9 .883 .562 5.186 52 255 .449 .47 80 4140 9220 38 46 270 278 -50 220 185 35 .41 206 21 2.437 1.047 -1.285 .066
19 10516 11562 187 162 10329 11400 11385 12647 199 173 11198 12485 0 0 3569 3728 76 73 100 100 100 100 21729 23683 .906 1.104 1.115 1.145 1.108 1.529 80 353 1.098 .97 100 4280 9230 38 48 283 293 0 13444 188 13256 1.283 14706 14517 .779 1.296 .36 .375
20 5171 4341 191 162 4980 4179 5123 4215 202 181 4932 4053 0 0 1617 1049 67 105 100 100 100 100 9159 8985 1.192 .839 .822 .861 .857 1.296 52 289 .803 .96 90 4420 9230 38 47 297 306 0 5048 188 4859 .976 4901 4713 1.025 .956 -.035 -.066

Total number of rows: 43104

Table truncated, full table size 9716 Kbytes.




Supplementary data files not provided
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