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Sample GSM95466 Query DataSets for GSM95466
Status Public on Feb 25, 2006
Title OV433 E3
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Characteristics CRH
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name CRH vs OV433 E3
Organism Homo sapiens
Characteristics CRH vs OV433 E3
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Drug_treatment, Taxol
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/29056.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 GPL2696
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
1 472 291 109 73 363 218 487 291 119 91 378 218 0 0 93 85 77 63 100 91 100 83 581 596 1.665 .601 .577 .563 .533 1.886 12 98 .641 .56 50 1710 8710 40 45 36 41 0 267 67 200 .551 267 200 1.815 .529 -.86 -.918
2 449 502 131 87 318 415 448 495 136 96 317 408 0 0 140 204 42 52 96 100 96 93 733 725 .766 1.305 1.287 1.277 1.335 1.693 32 170 1.48 .78 60 1840 8730 42 48 49 55 0 461 80 381 1.197 454 374 .835 1.181 .26 .24
3 2730 911 128 88 2602 823 2875 1000 130 95 2747 912 0 0 821 361 35 39 100 98 100 98 3425 3659 3.162 .316 .332 .286 .33 1.979 80 461 .313 .85 110 2010 8720 38 49 63 74 0 836 81 755 .29 917 837 3.446 .305 -1.785 -1.715
4 2614 4028 130 95 2484 3933 2739 3780 131 99 2609 3685 0 0 1271 2447 34 36 100 100 100 100 6417 6294 .632 1.583 1.412 1.376 1.668 2.008 52 234 1.797 .9 80 2150 8730 41 49 79 87 0 3695 87 3608 1.453 3468 3381 .688 1.296 .539 .374
5 792 938 135 100 657 838 775 1016 137 104 640 916 0 0 387 462 40 36 94 100 92 100 1495 1556 .784 1.275 1.431 1.22 1.193 2.028 52 277 1.311 .85 80 2290 8730 41 49 93 101 0 861 92 769 1.17 932 840 .855 1.313 .227 .393
6 294 220 124 104 170 116 276 236 125 107 152 132 0 0 77 84 38 37 100 83 91 58 286 284 1.466 .682 .868 .712 .811 3.024 12 104 .645 .51 50 2440 8720 41 46 109 114 0 202 95 106 .626 217 121 1.597 .797 -.676 -.328
7 1252 199 127 90 1125 109 1424 199 137 93 1297 109 0 0 493 68 56 35 96 82 94 67 1234 1406 10.321 .097 .084 .097 .102 1.85 52 262 .095 .74 80 2580 8730 41 49 122 130 0 183 83 100 .089 183 100 11.25 .077 -3.492 -3.697
8 2912 3049 127 90 2785 2959 1562 1714 136 95 1435 1624 0 0 2889 3015 48 36 90 96 85 94 5744 3059 .941 1.062 1.132 1.219 1.03 3.616 120 462 1.056 .92 120 2740 8730 39 51 136 148 0 2797 83 2715 .975 1572 1490 1.026 1.038 -.037 .054
9 844 1167 128 90 716 1077 884 1231 130 96 756 1141 0 0 335 514 36 38 100 100 100 100 1793 1897 .665 1.504 1.509 1.502 1.544 1.753 52 283 1.678 .85 90 2870 8720 39 48 150 159 0 1071 83 988 1.38 1129 1047 .725 1.385 .465 .47
10 411 189 138 99 273 90 393 184 142 99 255 85 0 0 152 60 40 33 90 81 90 65 363 340 3.033 .33 .333 .291 .358 1.942 32 158 .263 .58 60 3020 8730 42 48 167 173 0 173 91 83 .302 169 78 3.306 .306 -1.725 -1.709
11 2607 6493 132 94 2475 6399 2537 6471 135 99 2405 6377 0 0 958 2322 40 35 100 100 100 100 8874 8782 .387 2.585 2.652 2.667 2.725 1.442 80 424 2.788 .88 110 3170 8730 39 50 179 190 0 5957 86 5871 2.372 5937 5850 .422 2.433 1.246 1.283
12 1119 774 130 91 989 683 874 680 136 100 744 589 0 0 786 488 43 42 95 96 88 93 1672 1333 1.448 .691 .792 .738 .623 2.749 80 332 .613 .86 100 3320 8730 40 50 195 205 0 710 83 627 .634 624 540 1.578 .726 -.658 -.461
13 753 1042 134 93 619 949 857 1006 141 111 723 913 0 0 403 566 54 92 90 94 84 92 1568 1636 .652 1.533 1.263 1.689 1.725 2.178 52 251 1.605 .84 90 3450 8730 40 49 208 217 0 956 85 871 1.407 923 838 .711 1.159 .492 .212
14 948 215 131 96 817 119 299 188 137 114 168 92 0 0 1634 125 57 91 75 50 63 26 936 260 6.866 .146 .548 .372 .573 4.227 52 242 .065 .64 80 3590 8740 42 50 223 231 0 197 88 109 .134 172 84 7.483 .502 -2.904 -.993
15 4618 7563 121 84 4497 7479 4207 8422 123 89 4086 8338 0 0 3448 4822 48 43 93 100 88 100 11976 12424 .601 1.663 2.041 1.844 1.354 4.531 80 357 1.706 .8 100 3750 8740 41 51 238 248 0 6939 77 6861 1.526 7727 7650 .655 1.872 .61 .905
16 1709 2410 128 95 1581 2315 1590 2529 135 123 1462 2434 0 0 751 1076 60 143 100 100 98 100 3896 3896 .683 1.464 1.665 1.507 1.395 1.844 52 249 1.567 .85 80 3890 8720 40 48 253 261 0 2211 87 2124 1.343 2320 2233 .744 1.527 .426 .611
17 313 299 134 104 179 195 333 303 140 116 199 199 0 0 127 105 48 97 78 76 67 51 374 398 .918 1.089 1 1.099 .955 1.962 52 276 .934 .68 80 4030 8720 40 48 267 275 0 274 95 179 .999 278 183 1.001 .917 -.001 -.124
18 374 269 146 105 228 164 354 276 150 106 208 171 0 0 111 70 41 35 96 100 93 87 392 379 1.39 .719 .822 .678 .7 1.871 32 212 .577 .57 70 4180 8720 40 47 282 289 0 247 96 150 .66 253 157 1.515 .754 -.6 -.407
19 2367 2438 141 108 2226 2330 2577 2778 145 113 2436 2670 0 0 739 805 50 43 100 100 100 100 4556 5106 .955 1.047 1.096 1.049 1.074 1.642 80 490 1.091 .89 110 4330 8720 38 49 295 306 0 2237 99 2138 .96 2549 2450 1.041 1.006 -.058 .008
20 571 585 140 108 431 477 643 587 142 117 503 479 0 0 253 208 59 63 81 93 78 90 908 982 .904 1.107 .952 1.079 1.061 2.068 32 192 .953 .72 70 4480 8730 41 48 312 319 0 537 99 438 1.015 539 439 .985 .874 .022 -.195

Total number of rows: 43008

Table truncated, full table size 9309 Kbytes.




Supplementary data files not provided
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