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Sample GSM39913 Query DataSets for GSM39913
Status Public on Feb 21, 2005
Title Prostate 0845
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Prostate 0845
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-10/20949.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) pollack1@stanford.edu
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL1823
Series (1)
GSE2193 Normal_human_tissues

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
VALUE same as UNF_VALUE but with flagged values removed
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
UNF_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

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 UNF_VALUE
1 512 418 178 172 334 246 493 421 183 187 315 249 0 0 201 160 49 164 88 73 86 25 580 564 1.358 .737 .79 .676 .758 1.73 52 356 1.733 .49 90 1280 7700 37 46 47 56 0 303 125 178 .534 305 180 1.874 .573 -.906 -.804 -.906
2 403 403 185 182 218 221 430 406 186 189 245 224 0 0 130 138 45 62 90 86 84 78 439 469 .986 1.014 .914 .855 .94 1.95 52 274 1.08 .68 80 1430 7700 38 46 63 71 0 292 132 160 .735 294 162 1.361 .663 -.445 -.594 -.445
3 1950 2485 183 186 1767 2299 2163 2704 188 194 1980 2518 0 0 771 1077 47 60 98 100 96 98 4066 4498 .769 1.301 1.272 1.316 1.352 1.445 52 312 1.343 .95 90 1580 7700 37 46 77 86 0 1801 135 1666 .943 1959 1825 1.061 .922 -.085 -.118 -.085
4 3141 7737 179 182 2962 7555 1869 4179 188 190 1690 3997 0 0 3063 7739 47 59 90 98 87 95 10517 5687 .392 2.551 2.365 2.843 2.568 2.221 80 470 2.572 .98 110 1720 7700 36 47 90 101 0 5607 132 5475 1.848 3028 2896 .541 1.714 .886 .777 .886
5 560 686 196 183 364 503 572 763 199 193 376 580 0 0 238 312 45 57 84 84 84 81 867 956 .724 1.382 1.543 1.319 1.4 1.49 32 200 1.353 .91 70 1870 7710 39 46 107 114 0 497 133 364 1.001 553 420 .999 1.118 .002 .161 .002
6 385 330 190 169 195 161 376 315 194 180 186 146 0 0 132 98 46 59 86 90 82 59 356 332 1.211 .826 .785 .795 .788 2.045 52 279 .767 .71 80 2010 7700 38 46 121 129 0 239 122 117 .598 228 106 1.671 .569 -.741 -.814 -.741
7 1125 537 193 170 932 367 1195 582 202 181 1002 412 0 0 393 162 58 58 92 88 92 88 1299 1414 2.54 .394 .411 .392 .386 1.498 52 239 .354 .87 80 2160 7700 38 46 136 144 0 389 123 266 .285 422 299 3.505 .298 -1.809 -1.747 -1.809
8 5695 9544 186 165 5509 9379 5234 9505 193 174 5048 9340 0 0 4632 7033 49 59 87 100 83 96 14888 14388 .587 1.702 1.85 2.281 1.744 2.267 80 358 1.644 .96 100 2300 7700 37 47 149 159 0 6916 120 6796 1.234 6888 6768 .811 1.341 .303 .423 .303
9 1135 1675 181 164 954 1511 1275 1828 185 174 1094 1664 0 0 513 706 42 65 98 100 98 98 2465 2758 .631 1.584 1.521 1.703 1.541 1.624 52 262 1.561 .95 80 2440 7700 38 46 164 172 0 1214 119 1095 1.148 1325 1206 .871 1.102 .199 .14 .199
10 508 580 188 168 320 412 539 641 191 175 351 473 0 0 141 202 46 68 93 90 90 87 732 824 .777 1.288 1.348 1.203 1.292 1.771 32 219 1.384 .78 70 2590 7700 38 45 179 186 0 420 122 299 .933 464 343 1.072 .977 -.1 -.034 -.1
11 1407 1661 195 164 1212 1497 1425 1672 195 168 1230 1508 0 0 660 875 44 60 100 100 100 98 2709 2738 .81 1.235 1.226 1.166 1.172 1.481 52 294 1.298 .93 80 2740 7700 38 46 194 202 0 1204 119 1085 .895 1212 1093 1.117 .888 -.16 -.171 -.16
12 1553 1565 185 166 1368 1399 1582 1622 190 172 1397 1456 0 0 495 572 45 52 96 100 96 98 2767 2853 .978 1.023 1.042 1.008 1.032 1.384 52 264 1.058 .95 80 2890 7700 38 46 209 217 0 1134 120 1014 .741 1175 1055 1.349 .755 -.432 -.405 -.432
13 2026 2543 194 180 1832 2363 1199 1326 198 183 1005 1146 0 0 2027 2572 51 54 98 100 96 100 4195 2151 .775 1.29 1.14 1.358 1.212 2.206 52 246 1.307 .93 80 3030 7700 38 46 223 231 0 1843 130 1712 .935 961 830 1.07 .826 -.097 -.275 -.097
14 435 561 187 189 248 372 460 564 192 198 273 375 0 0 130 176 56 79 87 93 84 93 620 648 .667 1.5 1.374 1.497 1.389 1.682 32 213 1.684 .79 70 3170 7690 37 44 237 244 0 407 137 270 1.087 409 272 .92 .995 .12 -.007 .12
15 8797 12740 176 194 8621 12546 8912 13546 184 198 8736 13352 0 0 3241 4636 50 70 100 100 98 100 21167 22088 .687 1.455 1.528 1.572 1.487 1.542 52 350 1.458 .98 90 3320 7700 37 46 251 260 0 9232 141 9091 1.055 9816 9675 .948 1.108 .077 .147 .077
16 1980 5509 172 183 1808 5326 2073 5653 176 186 1901 5470 0 0 551 1712 41 54 98 100 96 100 7134 7371 .339 2.946 2.877 3.036 2.933 1.417 52 335 3.104 .96 90 3470 7700 37 46 266 275 0 3992 133 3859 2.135 4096 3964 .468 2.085 1.094 1.06 1.094
17 276 333 180 179 96 154 288 317 176 182 108 138 0 0 74 103 44 53 84 90 65 65 250 246 .623 1.604 1.278 1.276 1.569 2.4 32 218 1.923 .53 70 3620 7700 38 45 282 289 0 241 130 112 1.162 230 100 .86 .926 .217 -.111 .217
18 356 292 176 171 180 121 397 305 176 183 221 134 0 0 113 95 44 61 91 75 83 50 301 355 1.488 .672 .606 .482 .66 2.895 12 104 .677 .64 50 3760 7700 39 44 297 302 0 212 124 88 .487 221 97 2.053 .439 -1.038 -1.186 -1.038
19 932 1451 174 181 758 1270 943 1280 178 196 769 1099 0 0 485 788 43 73 94 98 94 96 2028 1868 .597 1.675 1.429 1.686 1.596 1.558 52 297 1.701 .94 80 3910 7700 38 46 311 319 0 1051 131 920 1.214 928 796 .824 1.036 .28 .05 .28
20 355 317 172 183 183 134 383 302 176 190 211 119 0 0 132 120 42 54 84 78 84 56 317 330 1.366 .732 .564 .559 .694 2.985 32 198 .767 .52 70 4050 7700 38 45 325 332 0 230 133 97 .531 219 86 1.885 .409 -.914 -1.291 -.914

Total number of rows: 43008

Table truncated, full table size 9417 Kbytes.




Supplementary data files not provided
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