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Sample GSM95443 Query DataSets for GSM95443
Status Public on Feb 25, 2006
Title Mesov E3
Sample type RNA
 
Channel 1
Source name CRH
Organism Homo sapiens
Characteristics CRH
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Mesov E3
Organism Homo sapiens
Characteristics Mesov E3
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Drug_treatment, Taxol
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27136.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
1 479 234 220 59 259 175 493 235 223 63 273 176 0 0 116 107 37 23 96 90 90 84 434 449 1.48 .676 .645 .568 .691 2.376 52 289 .699 .83 80 1670 8920 56 64 55 63 0 263 66 197 .759 264 198 1.317 .724 -.397 -.465
2 461 287 210 69 251 218 457 298 213 73 247 229 0 0 127 136 36 27 90 87 87 81 469 476 1.151 .869 .927 .698 .949 2.363 32 201 .921 .87 70 1810 8910 55 62 69 76 0 322 78 245 .976 335 257 1.025 1.042 -.035 .059
3 1263 251 199 62 1064 189 855 166 201 66 656 104 0 0 950 194 35 30 98 80 97 68 1253 760 5.63 .178 .159 .172 .183 2.009 80 450 .182 .85 110 1950 8910 53 64 81 92 0 282 70 212 .2 187 117 5.01 .178 -2.325 -2.489
4 1533 2043 202 66 1331 1977 1740 2310 203 74 1538 2244 0 0 764 1125 36 49 96 100 92 96 3308 3782 .673 1.485 1.459 1.54 1.471 1.672 52 326 1.523 .92 90 2090 8910 54 63 96 105 0 2296 74 2221 1.669 2596 2521 .599 1.639 .739 .713
5 599 309 206 71 393 238 599 331 212 77 393 260 0 0 187 122 48 34 100 87 93 84 631 653 1.651 .606 .662 .588 .645 1.812 32 208 .591 .85 70 2240 8900 54 61 112 119 0 347 80 267 .68 372 292 1.47 .743 -.555 -.428
6 335 188 200 66 135 122 316 178 202 71 116 112 0 0 99 99 40 26 80 84 65 69 257 228 1.107 .904 .966 .943 .908 1.814 52 267 .901 .81 80 2390 8910 55 63 127 135 0 211 74 137 1.015 200 126 .985 1.085 .022 .117
7 700 238 199 77 501 161 781 238 202 80 582 161 0 0 255 126 35 25 92 76 90 76 662 743 3.112 .321 .277 .261 .276 2.387 52 237 .312 .76 80 2530 8910 55 63 141 149 0 267 87 181 .361 267 181 2.77 .311 -1.47 -1.686
8 2182 3492 200 84 1982 3408 1625 2270 202 87 1425 2186 0 0 1674 2952 35 26 100 100 100 100 5390 3611 .582 1.719 1.534 1.643 1.803 1.722 80 370 1.773 .96 100 2670 8910 54 64 154 164 0 3924 94 3829 1.932 2551 2456 .518 1.724 .95 .785
9 639 768 198 86 441 682 626 716 202 87 428 630 0 0 154 370 34 27 100 98 100 98 1123 1058 .647 1.546 1.472 1.252 1.532 2.175 52 256 1.826 .9 80 2820 8910 55 63 170 178 0 863 97 766 1.738 804 708 .575 1.654 .797 .726
10 404 294 199 89 205 205 416 296 200 92 217 207 0 0 91 95 31 23 93 96 93 96 410 424 1 1 .954 .989 .983 1.652 32 145 .993 .81 60 2970 8910 56 62 186 192 0 330 100 230 1.124 333 233 .89 1.072 .168 .1
11 736 1004 198 97 538 907 442 369 199 102 244 272 0 0 592 1120 36 38 81 88 73 78 1445 516 .593 1.686 1.115 1.544 1.574 2.426 80 449 2.128 .85 110 3100 8900 52 63 196 207 0 1128 109 1019 1.894 415 306 .528 1.253 .922 .325
12 807 1023 195 101 612 922 830 1121 194 103 635 1020 0 0 358 548 35 35 96 98 96 94 1534 1655 .664 1.507 1.606 1.357 1.379 1.777 52 308 1.556 .93 90 3260 8910 54 63 213 222 0 1149 113 1036 1.693 1260 1146 .591 1.805 .759 .852
13 532 636 186 101 346 535 513 648 187 102 327 547 0 0 198 338 31 27 98 96 90 92 881 874 .647 1.546 1.673 1.35 1.395 1.808 52 287 1.713 .88 90 3400 8910 54 63 227 236 0 715 113 601 1.737 728 615 .576 1.88 .797 .91
14 301 241 186 110 115 131 312 258 188 112 126 148 0 0 68 94 31 32 81 81 81 71 246 274 .878 1.139 1.175 1.348 1.242 2.957 32 155 1.21 .71 60 3550 8900 55 61 244 250 0 271 124 147 1.28 290 166 .781 1.32 .356 .4
15 2369 4071 181 109 2188 3962 2681 4884 184 116 2500 4775 0 0 1038 2185 32 41 100 100 100 100 6150 7275 .552 1.811 1.91 1.67 1.755 1.436 80 477 1.97 .94 110 3700 8910 53 64 256 267 0 4574 122 4452 2.035 5488 5365 .491 2.146 1.025 1.102
16 1185 1409 181 119 1004 1290 1284 1511 181 123 1103 1392 0 0 420 678 31 35 100 96 98 92 2294 2495 .778 1.285 1.262 1.075 1.234 1.842 52 253 1.406 .93 80 3850 8910 55 63 273 281 0 1583 134 1449 1.444 1698 1564 .693 1.418 .53 .504
17 387 349 182 128 205 221 414 359 190 138 232 231 0 0 73 119 45 51 96 84 90 81 426 463 .928 1.078 .996 .97 1.089 1.677 32 205 1.223 .83 70 3980 8900 54 61 286 293 0 392 144 248 1.211 403 260 .826 1.119 .277 .162
18 345 335 169 118 176 217 335 337 174 120 166 219 0 0 125 176 38 41 87 81 81 75 393 385 .811 1.233 1.319 1.08 1.222 1.982 32 148 1.404 .83 60 4130 8900 55 61 302 308 0 376 133 244 1.385 379 246 .722 1.482 .47 .568
19 566 689 141 90 425 599 464 513 144 98 323 423 0 0 294 465 51 47 97 93 93 91 1024 746 .71 1.409 1.31 1.222 1.369 2.098 80 403 1.597 .88 100 4270 8900 53 63 314 324 0 774 101 673 1.584 576 475 .631 1.471 .663 .557
20 383 371 133 90 250 281 408 429 138 99 275 339 0 0 114 152 36 40 90 90 90 84 531 614 .89 1.124 1.233 .998 1.045 1.647 32 155 1.272 .88 60 4430 8900 55 61 332 338 0 417 101 316 1.263 482 381 .792 1.385 .337 .47

Total number of rows: 43008

Table truncated, full table size 9182 Kbytes.




Supplementary data files not provided
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