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Sample GSM90932 Query DataSets for GSM90932
Status Public on Aug 13, 2007
Title BC-M-330
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-330
Organism Homo sapiens
Characteristics BC-M-330
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50723.gif; format: GIF
Datafile type: GenePix Results 3
name: 50723_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
1 795 435 269 146 526 289 867 444 270 146 598 298 0 0 176 119 22 13 100 100 100 100 815 896 1.82 .549 .498 .526 .57 1.342 52 320 .56 .97 90 1110 4360 431 440 106 115 0 767 258 510 .969 783 526 1.032 .879 -.045 -.186 -.186
2 13885 3644 266 146 13619 3498 13724 3671 268 146 13458 3525 0 0 7471 1981 21 12 100 100 100 100 17117 16983 3.893 .257 .262 .258 .261 1.3 80 349 .257 .99 100 1250 4360 431 441 120 130 0 6428 258 6171 .453 6476 6218 2.207 .462 -1.142 -1.114 -1.114
3 12814 3575 265 145 12549 3430 14085 4207 264 145 13820 4062 0 0 6508 1743 19 13 100 100 100 100 15979 17882 3.659 .273 .294 .278 .274 1.244 52 255 .268 .99 80 1390 4360 432 440 135 143 0 6307 256 6051 .482 7422 7166 2.074 .519 -1.052 -.948 -.948
4 5507 420 257 144 5250 276 5368 395 258 144 5111 251 0 0 2834 152 20 13 100 100 100 98 5526 5362 19.022 .053 .049 .05 .053 1.401 52 324 .052 .97 90 1540 4350 430 439 149 158 0 741 254 487 .093 697 443 10.783 .087 -3.431 -3.529 -3.529
5 2887 3371 260 144 2627 3227 2933 3706 261 144 2673 3562 0 0 1028 1387 20 13 100 100 100 100 5854 6235 .814 1.228 1.333 1.161 1.234 1.276 52 313 1.261 .99 90 1690 4350 430 439 164 173 0 5947 254 5693 2.167 6538 6284 .461 2.351 1.116 1.233 1.233
6 910 377 263 143 647 234 978 390 269 146 715 247 0 0 192 84 67 25 100 100 100 98 881 962 2.765 .362 .345 .353 .357 1.286 52 275 .354 .96 80 1830 4360 432 440 179 187 0 665 252 413 .638 688 436 1.567 .609 -.648 -.715 -.715
7 2828 2087 250 141 2578 1946 3031 2239 253 142 2781 2098 0 0 1618 1148 22 12 100 100 100 100 4524 4879 1.325 .755 .754 .773 .747 1.438 52 251 .738 .99 80 1990 4360 432 440 195 203 0 3682 249 3433 1.332 3950 3701 .751 1.331 .413 .412 .412
8 1603 730 252 140 1351 590 1671 741 254 140 1419 601 0 0 567 283 20 13 100 98 100 98 1941 2020 2.29 .437 .424 .405 .427 1.349 80 342 .449 .98 100 2130 4350 430 440 208 218 0 1288 247 1041 .77 1307 1060 1.298 .747 -.376 -.421 -.421
9 2868 331 253 139 2615 192 3025 329 256 144 2772 190 0 0 1253 115 29 41 100 87 98 81 2807 2962 13.62 .073 .069 .068 .072 1.633 80 346 .074 .94 100 2270 4350 430 440 222 232 0 584 245 339 .13 580 335 7.721 .121 -2.949 -3.048 -3.048
10 3063 1827 251 140 2812 1687 3262 1898 256 144 3011 1758 0 0 601 414 47 32 100 100 100 100 4499 4769 1.667 .6 .584 .595 .609 1.119 52 264 .603 .99 90 2410 4350 430 439 236 245 0 3223 247 2976 1.058 3348 3101 .945 1.03 .082 .043 .043
11 12365 9241 250 142 12115 9099 12627 9351 257 146 12377 9209 0 0 4873 4134 49 43 100 100 100 100 21214 21586 1.331 .751 .744 .721 .76 1.246 80 370 .769 .99 100 2560 4350 430 440 251 261 0 16302 251 16051 1.325 16496 16245 .755 1.313 .406 .392 .392
12 14738 10656 242 139 14496 10517 14927 11339 250 143 14685 11200 0 0 3863 3361 48 46 100 100 100 100 25013 25885 1.378 .726 .763 .707 .727 1.204 52 300 .739 .99 90 2710 4350 430 439 266 275 0 18798 245 18553 1.28 20003 19758 .781 1.345 .356 .428 .428
13 6754 9309 243 139 6511 9170 6539 9164 245 141 6296 9025 0 0 2119 3245 23 24 100 100 100 100 15681 15321 .71 1.408 1.433 1.38 1.396 1.184 52 312 1.45 .99 90 2850 4350 430 439 280 289 0 16422 245 16177 2.485 16166 15921 .402 2.529 1.313 1.338 1.338
14 855 796 239 138 616 658 847 820 240 141 608 682 0 0 88 98 24 24 100 100 100 100 1274 1290 .936 1.068 1.122 1.067 1.084 1.123 52 312 1.074 .98 90 3000 4350 430 439 295 304 0 1404 243 1161 1.884 1447 1203 .531 1.979 .914 .985 .985
15 926 24328 239 135 687 24193 923 23406 240 137 684 23271 0 0 270 9574 20 15 100 100 100 100 24880 23955 .028 35.215 34.022 35.309 35.335 1.205 80 327 35.801 .99 100 3150 4350 430 440 310 320 0 42917 238 42679 62.123 41290 41052 .016 60.018 5.957 5.907 5.907
16 16520 11971 251 136 16269 11835 15940 11431 252 138 15689 11295 0 0 7128 5330 28 15 100 100 100 100 28104 26984 1.375 .727 .72 .716 .746 1.218 80 344 .731 .99 100 3300 4350 430 440 325 335 0 21118 240 20878 1.283 20165 19925 .779 1.27 .36 .345 .345
17 11528 7595 254 139 11274 7456 11932 8100 257 144 11678 7961 0 0 2722 2190 37 31 100 100 100 100 18730 19639 1.512 .661 .682 .647 .672 1.167 52 316 .672 .99 90 3440 4350 430 439 339 348 0 13398 245 13153 1.167 14289 14044 .857 1.203 .222 .266 .266
18 2553 18779 242 136 2311 18643 2759 20539 245 136 2517 20403 0 0 762 6894 24 14 100 100 100 100 20954 22920 .124 8.067 8.106 7.723 8.271 1.251 80 357 8.275 .99 100 3590 4350 430 440 354 364 0 33128 240 32888 14.231 36233 35993 .07 14.3 3.831 3.838 3.838
19 10189 4637 222 132 9967 4505 10280 4792 226 132 10058 4660 0 0 2688 1350 21 14 100 100 100 100 14472 14718 2.212 .452 .463 .442 .459 1.222 52 288 .454 .99 90 3730 4350 430 439 368 377 0 8180 233 7947 .797 8453 8221 1.254 .817 -.327 -.291 -.291
20 15589 5011 214 131 15375 4880 16045 5049 224 134 15831 4918 0 0 4195 1513 61 28 100 100 100 100 20255 20749 3.151 .317 .311 .312 .321 1.171 52 316 .318 .99 90 3870 4350 430 439 382 391 0 8840 231 8609 .56 8907 8676 1.786 .548 -.837 -.868 -.868

Total number of rows: 43200

Table truncated, full table size 10025 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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