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Sample GSM95467 Query DataSets for GSM95467
Status Public on Feb 25, 2006
Title 1A9 E1
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 IA9 E1
Organism Homo sapiens
Characteristics CRH vs IA9 E1
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Drug_treatment, Taxol
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/29057.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
1 391 247 115 65 276 182 403 251 126 72 288 186 0 0 80 97 58 47 100 87 100 81 458 474 1.516 .659 .646 .548 .653 1.971 32 230 .706 .78 70 1690 8620 38 45 21 28 0 252 66 186 .673 256 190 1.486 .659 -.572 -.602
2 449 197 117 65 332 132 452 203 123 67 335 138 0 0 130 60 49 23 100 93 100 90 464 473 2.515 .398 .412 .359 .376 2.081 32 209 .328 .78 70 1840 8650 41 48 36 43 0 201 66 135 .406 207 141 2.465 .42 -1.301 -1.25
3 3214 441 125 66 3089 375 3436 421 220 102 3311 355 0 0 903 212 1056 435 97 35 80 1 3464 3666 8.237 .121 .107 .102 .114 1.952 80 385 .19 .62 100 1990 8630 38 48 50 60 0 450 67 383 .124 430 362 8.073 .109 -3.013 -3.192
4 3372 3251 129 69 3243 3182 3533 3355 133 73 3404 3286 0 0 1730 1786 40 30 100 100 100 100 6425 6690 1.019 .981 .965 .973 .953 1.847 52 289 .999 .9 90 2130 8640 39 48 64 73 0 3317 70 3247 1.001 3423 3353 .999 .985 .002 -.022
5 815 278 122 71 693 207 830 287 137 75 708 216 0 0 258 88 81 28 100 96 100 94 900 924 3.348 .299 .305 .278 .285 1.804 52 302 .272 .85 80 2280 8640 40 48 80 88 0 284 72 211 .305 293 220 3.281 .311 -1.714 -1.684
6 235 145 116 62 119 83 230 129 129 62 114 67 0 0 43 50 79 22 81 90 15 84 202 181 1.434 .697 .588 .661 .721 1.924 32 167 .704 .59 60 2430 8640 41 47 96 102 0 148 63 85 .712 132 68 1.405 .6 -.491 -.738
7 1381 207 116 70 1265 137 1428 203 139 100 1312 133 0 0 489 64 144 318 100 0 98 0 1402 1445 9.234 .108 .101 .107 .106 1.56 52 289 .258 .29 90 2570 8650 40 49 108 117 0 211 71 140 .111 207 136 9.049 .103 -3.178 -3.273
8 3070 4952 121 73 2949 4879 3022 5318 374 148 2901 5245 0 0 2410 3374 2267 653 55 82 32 73 7828 8146 .604 1.654 1.808 1.743 1.478 2.188 80 349 1.59 .92 100 2720 8650 40 50 123 133 0 5053 74 4979 1.688 5427 5352 .592 1.845 .756 .884
9 870 720 126 65 744 655 945 770 425 123 819 705 0 0 302 261 2535 522 0 69 0 7 1399 1524 1.136 .88 .861 .886 .814 1.482 52 276 .884 .9 80 2860 8640 40 48 138 146 0 735 66 668 .898 786 719 1.113 .878 -.155 -.187
10 435 183 130 71 305 112 448 178 132 74 318 107 0 0 127 47 35 25 100 100 96 90 417 425 2.723 .367 .336 .377 .413 1.753 32 186 .291 .69 70 3010 8640 40 47 153 160 0 187 72 114 .375 182 109 2.669 .343 -1.416 -1.542
11 2033 3802 127 72 1906 3730 2199 4234 131 75 2072 4162 0 0 1202 2393 37 28 89 98 86 95 5636 6234 .511 1.957 2.009 1.955 2.079 2.34 120 499 2.2 .87 120 3150 8630 37 49 165 177 0 3880 73 3806 1.997 4320 4247 .501 2.05 .998 1.035
12 1361 2022 132 79 1229 1943 1466 1989 134 79 1334 1910 0 0 666 952 37 29 96 100 94 98 3172 3244 .633 1.581 1.432 1.739 1.564 2.178 52 217 1.558 .95 80 3290 8650 41 49 181 189 0 2063 81 1983 1.613 2030 1949 .62 1.461 .69 .547
13 861 1005 134 80 727 925 866 1042 138 82 732 962 0 0 247 288 37 28 100 100 100 100 1652 1694 .786 1.272 1.314 1.282 1.314 1.332 52 263 1.275 .93 80 3440 8640 40 48 196 204 0 1026 82 944 1.298 1063 982 .77 1.341 .377 .423
14 305 193 137 68 168 125 310 187 142 73 173 119 0 0 63 48 41 27 96 100 90 100 293 292 1.344 .744 .688 .776 .765 1.936 32 155 .573 .64 60 3590 8650 42 48 212 218 0 197 69 128 .759 191 121 1.317 .702 -.397 -.511
15 4900 9406 128 79 4772 9327 5467 11019 132 83 5339 10940 0 0 2242 4342 38 33 100 100 100 100 14099 16279 .512 1.955 2.049 2.019 1.922 1.688 80 381 2.008 .95 100 3730 8640 39 49 224 234 0 9598 81 9517 1.994 11244 11163 .501 2.091 .996 1.064
16 1997 2220 129 85 1868 2135 2084 2317 141 98 1955 2232 0 0 632 774 58 66 100 100 100 100 4003 4187 .875 1.143 1.142 1.134 1.103 1.262 52 259 1.177 .95 80 3880 8630 39 47 240 248 0 2265 87 2179 1.166 2364 2278 .857 1.165 .222 .22
17 397 248 134 79 263 169 388 238 145 87 254 159 0 0 117 64 68 48 100 96 93 90 432 413 1.556 .643 .626 .65 .68 1.898 32 212 .497 .69 70 4020 8640 40 47 254 261 0 253 81 172 .656 243 162 1.525 .639 -.609 -.647
18 322 243 101 71 221 172 325 218 114 76 224 147 0 0 81 75 75 35 93 100 81 96 393 371 1.285 .778 .656 .785 .75 2.214 32 176 .582 .55 60 4170 8640 41 47 270 276 0 248 72 176 .794 222 150 1.259 .67 -.332 -.579
19 819 962 63 52 756 910 681 646 75 68 618 594 0 0 809 891 39 122 73 67 69 63 1666 1212 .831 1.204 .961 1.293 1.15 2.563 52 274 1.205 .9 90 4340 8640 39 48 285 294 0 982 53 929 1.228 659 606 .814 .981 .297 -.028
20 95 80 71 53 24 27 63 65 94 64 -8 12 0 0 87 73 59 37 11 19 11 5 51 4 .889 1.125 null .877 1.059 3.421 52 216 .856 .71 80 4450 8630 39 47 297 305 0 82 54 28 1.148 66 12 .871 null .199 null

Total number of rows: 43008

Table truncated, full table size 9250 Kbytes.




Supplementary data files not provided
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