NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM90964 Query DataSets for GSM90964
Status Public on Aug 13, 2007
Title BC-M-020
Sample type RNA
 
Channel 1
Source name Stratagene ref aRNA
Organism Homo sapiens
Characteristics Stratagene ref aRNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name BC-M-020
Organism Homo sapiens
Characteristics BC-M-020
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50739.gif; format: GIF
Datafile type: GenePix Results 3
name: 50739_Datafile type
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 Jan 06, 2006
Last update date Aug 13, 2007
Contact name Therese Sorlie
E-mail(s) tsorlie@labmed.uio.no
Phone +4722934418
Fax +4722934440
Organization name The Norwegian Radium Hospital
Department Genetics
Street address Montebello
City Oslo
ZIP/Postal code 0310
Country Norway
 
Platform ID GPL3319
Series (1)
GSE3985 Micrometastasis primary tumors

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 same as UNF_VALUE but with flagged values removed
UNF_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 UNF_VALUE
1 562 328 189 145 373 183 496 322 198 148 307 177 0 0 590 162 90 33 92 94 80 88 556 484 2.038 .491 .577 .561 .59 1.39 52 320 .121 .84 90 1490 3810 376 385 144 153 0 408 180 228 .611 401 220 1.638 .718 -.712 -.479 -.479
2 11930 1481 204 148 11726 1333 13390 1663 208 150 13186 1515 0 0 6073 688 32 16 100 100 100 100 13059 14701 8.797 .114 .115 .115 .114 1.266 80 347 .113 .99 100 1640 3810 376 386 159 169 0 1843 184 1659 .141 2070 1886 7.068 .143 -2.821 -2.806 -2.806
3 6111 3456 210 151 5901 3305 6552 3528 213 152 6342 3377 0 0 3627 2094 31 16 100 100 100 100 9206 9719 1.785 .56 .532 .545 .563 1.288 80 325 .564 .99 100 1790 3810 376 386 174 184 0 4301 188 4113 .697 4391 4203 1.435 .663 -.521 -.594 -.594
4 3031 691 214 153 2817 538 2729 668 219 155 2515 515 0 0 1914 377 42 20 100 95 98 95 3355 3030 5.236 .191 .205 .18 .196 1.481 80 337 .19 .98 100 1930 3800 375 385 188 198 0 860 190 670 .238 831 641 4.207 .255 -2.073 -1.972 -1.972
5 2082 4926 215 156 1867 4770 2339 5860 225 168 2124 5704 0 0 643 1827 67 83 100 100 100 100 6637 7828 .391 2.555 2.685 2.491 2.561 1.217 52 289 2.641 .98 90 2070 3800 375 384 202 211 0 6131 194 5937 3.18 7293 7099 .314 3.342 1.669 1.741 1.741
6 647 347 198 157 449 190 658 357 201 161 460 200 0 0 120 57 39 50 100 100 100 92 639 660 2.363 .423 .435 .415 .431 1.27 52 276 .403 .95 80 2220 3810 377 385 218 226 0 432 195 236 .527 444 249 1.899 .541 -.925 -.886 -.886
7 2247 2948 207 163 2040 2785 2437 2942 209 164 2230 2779 0 0 929 1193 30 17 100 100 98 100 4825 5009 .732 1.365 1.246 1.457 1.387 1.421 52 289 1.343 .98 90 2370 3810 376 385 232 241 0 3669 203 3466 1.699 3662 3459 .589 1.551 .765 .633 .633
8 981 1770 204 161 777 1609 1064 1881 212 164 860 1720 0 0 271 545 44 26 100 100 100 100 2386 2580 .483 2.071 2 2.092 2.034 1.241 80 370 2.089 .97 110 2510 3810 375 386 245 256 0 2203 200 2003 2.577 2341 2141 .388 2.489 1.366 1.316 1.316
9 1944 662 188 156 1756 506 2053 697 193 158 1865 541 0 0 560 165 41 20 100 100 100 100 2262 2406 3.47 .288 .29 .289 .29 1.183 80 309 .294 .84 100 2660 3810 376 386 261 271 0 824 194 630 .359 867 673 2.788 .361 -1.479 -1.47 -1.47
10 1713 2767 189 158 1524 2609 1858 3032 193 161 1669 2874 0 0 426 798 24 24 100 100 100 100 4133 4543 .584 1.712 1.722 1.684 1.717 1.164 80 371 1.744 .99 110 2800 3800 374 385 274 285 0 3444 197 3247 2.131 3774 3577 .469 2.143 1.091 1.1 1.1
11 7471 28841 183 157 7288 28684 8068 31821 188 162 7885 31664 0 0 1802 8432 23 44 100 100 100 100 35972 39549 .254 3.936 4.016 3.835 3.988 1.19 80 397 4.031 .99 110 2950 3800 374 385 289 300 0 35895 195 35700 4.898 39604 39408 .204 4.998 2.292 2.321 2.321
12 4889 17695 183 156 4706 17539 4903 17670 186 160 4720 17514 0 0 2291 8633 21 45 100 100 100 100 22245 22234 .268 3.727 3.711 3.853 3.683 1.24 80 330 3.774 .99 100 3100 3810 376 386 305 315 0 22023 194 21829 4.638 21992 21798 .216 4.618 2.214 2.207 2.207
13 4051 9269 183 155 3868 9114 4333 9946 200 159 4150 9791 0 0 1522 3886 161 44 100 100 100 100 12982 13941 .424 2.356 2.359 2.285 2.361 1.217 80 395 2.408 .99 110 3240 3800 374 385 318 329 0 11536 193 11343 2.933 12379 12186 .341 2.936 1.552 1.554 1.554
14 543 684 179 152 364 532 539 694 192 157 360 542 0 0 63 116 126 46 100 100 93 100 896 902 .684 1.462 1.506 1.441 1.458 1.187 80 343 1.504 .97 100 3390 3800 375 385 334 344 0 851 189 662 1.819 864 675 .55 1.874 .863 .906 .906
15 628 15503 174 150 454 15353 644 16049 175 152 470 15899 0 0 129 3510 16 19 100 100 100 100 15807 16369 .03 33.817 33.828 34.776 33.753 1.207 80 354 33.709 .98 110 3540 3810 375 386 348 359 0 19295 187 19108 42.088 19974 19788 .024 42.101 5.395 5.396 5.396
16 11000 10835 175 151 10825 10684 11376 11350 178 153 11201 11199 0 0 1950 2532 20 20 100 100 100 100 21509 22400 1.013 .987 1 .965 1.006 1.155 80 387 1.006 .99 110 3690 3800 374 385 363 374 0 13485 188 13297 1.228 14126 13938 .814 1.244 .297 .315 .315
17 6839 10340 183 153 6656 10187 7350 10800 186 156 7167 10647 0 0 2131 3512 22 21 100 100 100 100 16843 17814 .653 1.53 1.486 1.497 1.538 1.176 80 353 1.551 .99 100 3830 3800 375 385 378 388 0 12869 190 12679 1.905 13441 13251 .525 1.849 .93 .887 .887
18 2831 7476 186 153 2645 7323 2848 7632 204 197 2662 7479 0 0 283 873 97 274 100 100 100 100 9968 10141 .361 2.769 2.81 2.764 2.763 1.055 52 288 2.813 .99 90 3970 3800 375 384 392 401 0 9304 190 9114 3.446 9499 9308 .29 3.497 1.785 1.806 1.806
19 7293 5616 185 148 7108 5468 7395 5908 204 186 7210 5760 0 0 3093 2404 91 247 100 100 100 100 12576 12970 1.3 .769 .799 .748 .755 1.227 80 361 .769 .99 100 4130 3800 375 385 408 418 0 6990 184 6805 .957 7353 7169 1.044 .994 -.063 -.008 -.008
20 10410 7050 182 148 10228 6902 11574 7699 181 147 11392 7551 0 0 4026 2978 22 17 100 100 100 100 17130 18943 1.482 .675 .663 .626 .68 1.344 80 319 .685 .99 100 4280 3800 375 385 423 433 0 8774 184 8590 .84 9582 9398 1.191 .825 -.252 -.278 -.278

Total number of rows: 43200

Table truncated, full table size 10049 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap