NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM13768 Query DataSets for GSM13768
Status Public on Feb 12, 2004
Title KM109 t=0(1) t=4(2) batch II
Sample type RNA
 
Channel 1
Source name KM109 t=0
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name KM109 t=4
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Timecourse experiment hybridized to human oligo array part II. Healthy human primary myoblasts (KM109) just before fusion (channel 1, t=0) and four days after fusion induction (channel 2, t=4).
 
Submission date Dec 16, 2003
Last update date Nov 22, 2005
Contact name Ellen Sterrenburg
E-mail(s) E.sterrenburg@lumc.nl
Phone +31 71 527 6611
Organization name Leiden University Medical Center
Department Center for Human and Clinical Genetics
Lab Center for Human and Clinical Genetics
Street address Wassenaarseweg 72
City Leiden
ZIP/Postal code 2333 AL
Country Netherlands
 
Platform ID GPL784
Series (1)
GSE909 KM109_Human oligo batch II

Data table header descriptions
ID_REF
VALUE same as UNF_VALUE but with flagged values removed
P-value P-value of the difference (Rosetta Resolver)
Dia. Diameter of the spot
F1 Median Intensity target sample t=0
F1 Mean Mean signal intensity target sample t0
F1 SD Standard deviation of the intensity
B1 Median Median background of target sample
B1 Mean Mean background of target sample
B1 SD standard deviation of the background
% > B1+1SD Percentage of pixels that have a higher intensity than the background plus 1 SD
% > B1+2SD Percentage of pixels that is higher than the backgound plus 2 SD
F1 % Sat. Percentage saturated pixels
F2 Median Intensity target sample t=0
F2 Mean Mean signal intensity target sample t0
F2 SD Standard deviation of the intensity
B2 Median Background of reference sample
B2 Mean Mean background
B2 SD Standard deviation of the background
% > B2+1SD Percentage of pixels that have a higher signal than the background plus 1 SD
% > B2+2SD Percentage of pixels that have a higher signal than the background plus 2 SD
F2 % Sat. Percentage saturated pixels
Ratio of Medians Ratio of median intensities
Ratio of Means Ratio of mean intensities
Median of Ratios Median of ratios
Mean of Ratios Mean of ratios
Ratios SD Standard deviation
Rgn Ratio Regression ratio is determined by computing a linear regression between the population of pixels represented by wavelength 1 and wavelength 2
Rgn Rē Coefficient of determination provides a measure of the level of accuracy of the fit of the linear regression curve
F Pixels Number of pixels in the foreground
B Pixels Number of pixels in the background
Sum of Medians Sum of medians
Sum of Means Sum of means
Log Ratio Log ratio
F1 Median - B1 Median intensity of channel 1 minus the local background
F2 Median - B2 Median intensity of channel 2 minus the local background
F1 Mean - B1 Median intensity of target minus the local background
F2 Mean - B2 Median intensity of the reference sample minus the local background
Flags Negative number means the spot is bad or not found
UNF_VALUE normalized log10 ratio of channel 1 divided by channel two (ratio profiles, Rosetta Resolver)

Data table
ID_REF VALUE P-value Dia. F1 Median F1 Mean F1 SD B1 Median B1 Mean B1 SD % > B1+1SD % > B1+2SD F1 % Sat. F2 Median F2 Mean F2 SD B2 Median B2 Mean B2 SD % > B2+1SD % > B2+2SD F2 % Sat. Ratio of Medians Ratio of Means Median of Ratios Mean of Ratios Ratios SD Rgn Ratio Rgn Rē F Pixels B Pixels Sum of Medians Sum of Means Log Ratio F1 Median - B1 F2 Median - B2 F1 Mean - B1 F2 Mean - B2 Flags UNF_VALUE
1 0.48826 200 240 245 41 219 297 1557 0 0 0 350 355 49 306 336 297 0 0 0 0.477 0.531 0.528 0.581 3.237 2.305 0.117 316 2066 65 75 -1.067 21 44 26 49 -50 0.14183
2 -0.24246 0.1674 130 232 237 36 189 198 68 29 1 0 350 354 33 277 280 54 73 20 0 0.589 0.623 0.644 0.542 2.229 0.335 0.321 120 914 116 125 -0.764 43 73 48 77 0 -0.24246
3 2 1 180 232 244 92 178 700 5142 0 0 0 356 395 353 273 754 5175 0 0 0 0.651 0.541 0.619 0.578 2.256 0.943 0.913 256 1606 137 188 -0.62 54 83 66 122 0 2
4 -0.29822 0.00679 160 208 209 22 174 178 31 54 7 0 343 347 27 268 275 36 96 52 0 0.453 0.443 0.453 0.398 1.895 0.626 0.316 208 1314 109 114 -1.141 34 75 35 79 0 -0.29822
5 0.09931 0.32066 160 547 600 190 172 175 23 99 99 0 479 499 95 262 262 17 100 100 0 1.728 1.806 1.771 1.748 1.623 1.898 0.869 208 1353 592 665 0.789 375 217 428 237 0 0.09931
6 0.01798 0.85732 160 532 527 163 167 169 20 100 98 0 503 504 91 258 257 20 100 100 0 1.49 1.463 1.439 1.362 1.543 1.55 0.894 208 1315 610 606 0.575 365 245 360 246 0 0.01798
7 1 200 181 181 17 164 166 27 26 2 0 291 291 22 256 255 25 68 19 0 0.486 0.486 0.539 0.505 2.706 0.577 0.233 316 1787 52 52 -1.042 17 35 17 35 -75 0.21729
8 1 200 183 185 27 163 165 30 25 2 0 289 290 27 253 254 33 53 3 0 0.556 0.595 0.625 0.597 2.424 1.195 0.095 316 1755 56 59 -0.848 20 36 22 37 -75 0.21729
9 -0.21819 0.02912 200 307 308 42 163 164 23 99 98 0 425 435 60 254 254 19 100 100 0 0.842 0.801 0.81 0.794 1.348 0.619 0.675 316 1708 315 326 -0.248 144 171 145 181 0 -0.21819
10 -0.21592 0.03083 200 260 259 26 162 163 15 98 98 0 390 388 22 250 252 18 100 100 0 0.7 0.703 0.688 0.676 1.422 0.725 0.799 316 1739 238 235 -0.515 98 140 97 138 0 -0.21592
11 -0.28902 0.00385 210 227 229 24 161 162 17 98 93 0 369 369 21 247 248 17 99 99 0 0.541 0.557 0.548 0.521 1.533 0.57 0.677 316 1679 188 190 -0.886 66 122 68 122 0 -0.28902
12 -0.21121 0.03468 220 264 262 33 161 163 19 99 95 0 391 387 30 247 249 18 100 98 0 0.715 0.721 0.721 0.698 1.45 0.76 0.778 392 1738 247 241 -0.483 103 144 101 140 0 -0.21121
13 -0.17804 0.07501 210 276 276 34 169 171 24 99 95 0 390 390 29 254 255 21 100 100 0 0.787 0.787 0.777 0.762 1.324 0.941 0.649 316 1644 243 243 -0.346 107 136 107 136 0 -0.17804
14 -0.18945 0.05817 220 273 275 30 172 174 28 98 94 0 392 390 28 255 256 20 99 98 0 0.737 0.763 0.761 0.749 1.369 0.831 0.714 392 1711 238 238 -0.44 101 137 103 135 0 -0.18945
15 -0.2576 0.01 220 264 264 30 173 200 131 7 0 0 387 384 30 257 274 74 94 15 0 0.7 0.717 0.722 0.702 1.528 0.749 0.679 392 1980 221 218 -0.515 91 130 91 127 0 -0.2576
16 -0.16189 0.10548 210 330 331 48 185 191 55 99 78 0 448 450 64 284 290 36 100 99 0 0.884 0.88 0.878 0.868 1.291 0.923 0.666 316 1741 309 312 -0.178 145 164 146 166 0 -0.16189
17 -0.33455 0.83859 200 343 334 52 172 291 1861 0 0 0 442 431 53 273 334 1657 0 0 0 1.012 1.025 1.023 1.027 1.365 1.018 0.819 316 1617 340 320 0.017 171 169 162 158 0 -0.33455
18 1 200 228 229 23 162 711 5298 0 0 0 375 374 18 259 770 5332 0 0 0 0.569 0.583 0.575 0.553 1.507 0.993 0.931 316 1513 182 182 -0.814 66 116 67 115 0
19 -0.19444 0.05185 200 262 260 30 163 165 23 97 95 0 384 386 31 256 257 21 100 100 0 0.773 0.746 0.743 0.713 1.583 0.739 0.799 316 1549 227 227 -0.371 99 128 97 130 0 -0.19444
20 -0.29478 0.0032 210 234 235 24 165 166 20 98 91 0 384 382 21 257 257 21 100 100 0 0.543 0.56 0.552 0.536 1.443 0.576 0.682 316 1539 196 195 -0.88 69 127 70 125 0 -0.29478

Total number of rows: 10800

Table truncated, full table size 1812 Kbytes.




Supplementary data files not provided

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap