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Sample GSM95448 Query DataSets for GSM95448
Status Public on Feb 25, 2006
Title ES-2 E
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Characteristics CRH
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name ES-2 E
Organism Homo sapiens
Characteristics ES-2 E
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Drug_treatment, Taxol
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27137.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 Feb 03, 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 GPL3305
Series (1)
GSE4173 Taxane-selected ovarian cancer cell lines

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
1 458 451 86 76 372 375 471 447 92 81 385 371 0 0 194 218 91 29 94 98 78 92 747 756 .992 1.008 .964 .945 .982 1.843 52 306 1.05 .91 80 1630 8620 42 50 51 59 0 490 83 408 1.096 486 403 .913 1.047 .132 .067
2 449 657 93 86 356 571 494 717 100 102 401 631 0 0 180 309 51 69 90 90 87 84 927 1032 .623 1.604 1.574 1.401 1.694 1.939 32 186 1.705 .92 70 1790 8610 41 48 67 74 0 714 93 621 1.743 779 686 .574 1.71 .802 .774
3 1983 1707 87 81 1896 1626 1722 1256 91 89 1635 1175 0 0 1373 1335 34 48 100 96 98 91 3522 2810 1.166 .858 .719 .759 .776 1.965 80 439 .922 .94 110 1920 8620 40 51 78 89 0 1855 88 1767 .932 1365 1277 1.073 .781 -.101 -.356
4 2765 3634 83 72 2682 3562 2681 3502 87 75 2598 3430 0 0 1719 2407 21 25 100 100 100 98 6244 6028 .753 1.328 1.32 1.147 1.271 1.848 52 258 1.373 .96 80 2070 8620 42 50 95 103 0 3950 78 3872 1.444 3807 3728 .693 1.435 .53 .521
5 600 522 83 73 517 449 647 505 85 75 564 432 0 0 360 335 19 20 92 90 90 84 966 996 1.151 .868 .766 .874 .906 2.072 52 258 .894 .95 80 2220 8620 42 50 110 118 0 567 79 488 .944 549 470 1.059 .833 -.083 -.264
6 254 264 84 71 170 193 212 229 84 72 128 158 0 0 120 126 18 20 96 96 93 93 363 286 .881 1.135 1.234 1.266 1.152 1.921 32 164 1.357 .85 60 2360 8620 43 49 125 131 0 287 77 210 1.234 249 172 .81 1.342 .303 .424
7 1181 312 85 73 1096 239 1434 317 91 73 1349 244 0 0 632 193 34 24 92 84 90 71 1335 1593 4.586 .218 .181 .186 .192 2.292 52 293 .234 .88 90 2510 8610 40 49 138 147 0 339 79 260 .237 345 265 4.219 .197 -2.077 -2.347
8 3986 6337 85 71 3901 6266 3902 4793 89 74 3817 4722 0 0 3255 5502 28 22 95 98 93 98 10167 8539 .623 1.606 1.237 1.527 1.614 1.713 80 382 1.673 .97 100 2650 8620 41 51 152 162 0 6888 77 6811 1.746 5210 5133 .573 1.345 .804 .427
9 772 961 83 69 689 892 786 1048 85 70 703 979 0 0 322 480 18 21 100 100 100 100 1581 1682 .772 1.295 1.393 1.184 1.227 1.591 52 262 1.376 .94 80 2800 8620 42 50 168 176 0 1045 75 970 1.407 1139 1064 .711 1.514 .493 .598
10 282 220 87 77 195 143 278 202 90 79 191 125 0 0 115 106 23 26 93 87 84 75 338 316 1.364 .733 .654 .643 .727 2.241 32 190 .836 .85 70 2940 8610 41 48 182 189 0 239 84 155 .797 220 136 1.255 .711 -.327 -.491
11 1239 1938 86 79 1153 1859 687 1044 88 83 601 965 0 0 1141 1848 24 26 100 100 100 98 3012 1566 .62 1.612 1.606 1.568 1.605 1.62 80 408 1.598 .95 110 3090 8620 40 51 195 206 0 2107 86 2021 1.753 1135 1049 .571 1.745 .809 .803
12 1278 1428 88 78 1190 1350 1434 1461 90 80 1346 1383 0 0 755 886 22 23 92 92 90 90 2540 2729 .881 1.134 1.027 1.111 1.071 1.575 52 243 1.166 .94 80 3230 8610 41 49 211 219 0 1552 85 1467 1.233 1588 1503 .811 1.117 .302 .159
13 812 935 96 87 716 848 798 899 103 102 702 812 0 0 252 389 39 68 100 100 100 96 1564 1514 .844 1.184 1.157 1.116 1.126 1.368 32 202 1.324 .93 70 3380 8610 41 48 226 233 0 1016 95 922 1.287 977 883 .777 1.257 .364 .33
14 261 268 94 93 167 175 260 246 95 96 166 153 0 0 81 105 20 29 93 96 93 87 342 319 .954 1.048 .922 .965 .996 1.599 32 148 1.184 .83 60 3530 8610 42 48 242 248 0 291 101 190 1.139 267 166 .878 1.002 .188 .003
15 5160 8640 92 101 5068 8539 5976 10400 111 153 5884 10299 0 0 2437 4129 111 307 98 98 98 94 13607 16183 .594 1.685 1.75 1.671 1.663 1.283 52 321 1.727 .97 90 3660 8610 40 49 253 262 0 9391 110 9282 1.831 11304 11195 .546 1.903 .873 .928
16 1690 2054 95 99 1595 1955 1952 2400 105 117 1857 2301 0 0 720 955 70 151 96 90 94 86 3550 4158 .816 1.226 1.239 1.147 1.213 1.494 52 328 1.25 .97 90 3820 8610 40 49 269 278 0 2233 108 2125 1.332 2609 2501 .751 1.347 .414 .43
17 320 371 93 87 227 284 318 373 98 92 225 286 0 0 73 122 26 34 100 100 100 93 511 511 .799 1.251 1.271 1.145 1.23 1.604 32 203 1.26 .89 70 3960 8610 41 48 284 291 0 403 95 309 1.36 405 311 .735 1.382 .443 .466
18 264 270 95 91 169 179 264 277 98 95 169 186 0 0 65 88 29 28 100 93 93 93 348 355 .944 1.059 1.101 .967 .984 2.019 32 193 1.112 .8 70 4110 8610 41 48 299 306 0 293 99 195 1.151 301 202 .869 1.196 .203 .259
19 880 1209 89 88 791 1121 663 1008 93 92 574 920 0 0 730 1032 28 34 85 81 82 78 1912 1494 .706 1.417 1.603 1.303 1.398 2.15 120 519 1.437 .93 120 4260 8610 39 51 312 324 0 1314 96 1218 1.54 1096 1000 .649 1.742 .623 .801
20 458 412 93 88 365 324 484 428 98 93 391 340 0 0 144 147 29 45 93 96 93 90 689 731 1.127 .888 .87 .898 .871 1.503 32 178 .906 .9 70 4410 8610 41 48 329 336 0 448 96 352 .965 465 370 1.036 .945 -.052 -.081

Total number of rows: 43008

Table truncated, full table size 9290 Kbytes.




Supplementary data files not provided
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