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Sample GSM90984 Query DataSets for GSM90984
Status Public on Aug 13, 2007
Title BC-M-246
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-246
Organism Homo sapiens
Characteristics BC-M-246
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49771.gif; format: GIF
Datafile type: GenePix Results 3
name: 49771_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 GPL3315
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
1 218 331 88 102 130 229 228 348 97 112 140 246 0 0 48 91 48 47 90 100 75 84 359 386 .568 1.762 1.757 1.734 1.808 1.324 32 195 1.831 .93 70 1350 8820 878 885 131 138 0 627 193 434 3.339 660 466 .299 3.331 1.74 1.736 1.736
2 8529 839 86 101 8443 738 8688 917 89 105 8602 816 0 0 3153 312 20 26 100 100 100 100 9181 9418 11.44 .087 .095 .082 .087 1.273 52 338 .088 .98 90 1500 8810 876 885 145 154 0 1591 191 1399 .166 1738 1547 6.035 .18 -2.593 -2.475 -2.475
3 858 662 83 97 775 565 842 673 85 100 759 576 0 0 288 234 15 24 100 100 100 100 1340 1335 1.372 .729 .759 .689 .705 1.322 32 214 .768 .97 70 1650 8810 877 884 161 168 0 1255 184 1071 1.382 1276 1092 .724 1.439 .467 .525 .525
4 875 384 82 96 793 288 890 402 88 100 808 306 0 0 248 98 33 17 100 100 100 96 1081 1114 2.753 .363 .379 .35 .356 1.418 32 208 .345 .96 70 1790 8810 877 884 175 182 0 728 182 546 .688 762 580 1.452 .718 -.539 -.478 -.478
5 3573 2367 79 98 3494 2269 3700 2445 83 102 3621 2347 0 0 1589 1023 28 21 100 100 100 100 5763 5968 1.54 .649 .648 .646 .642 1.258 52 330 .644 .99 90 1930 8810 876 885 188 197 0 4487 186 4301 1.231 4635 4449 .812 1.229 .3 .297 .297
6 372 395 81 102 291 293 375 412 85 105 294 310 0 0 93 80 21 21 100 100 100 100 584 604 .993 1.007 1.054 1.018 .941 1.413 32 212 1.042 .94 70 2080 8810 877 884 204 211 0 749 193 555 1.909 781 588 .524 1.999 .933 .999 .999
7 2690 1316 82 103 2608 1213 2724 1377 83 106 2642 1274 0 0 973 419 14 19 100 100 100 100 3821 3916 2.15 .465 .482 .475 .48 1.215 52 336 .455 .98 90 2230 8810 876 885 218 227 0 2495 195 2300 .882 2610 2415 1.134 .914 -.182 -.13 -.13
8 277 390 80 101 197 289 276 408 81 102 196 307 0 0 62 93 10 13 98 100 98 100 486 503 .682 1.467 1.566 1.477 1.477 1.473 52 264 1.484 .97 80 2380 8810 877 885 234 242 0 739 191 548 2.781 773 582 .36 2.969 1.476 1.57 1.57
9 1379 372 78 99 1301 273 1407 397 79 100 1329 298 0 0 294 88 15 12 100 100 100 100 1574 1627 4.766 .21 .224 .202 .212 1.312 52 311 .205 .97 90 2520 8810 876 885 247 256 0 705 188 518 .398 753 565 2.514 .425 -1.33 -1.234 -1.234
10 353 291 77 97 276 194 360 299 79 100 283 202 0 0 76 61 16 12 100 100 100 100 470 485 1.423 .703 .714 .684 .726 1.318 52 250 .697 .96 80 2680 8810 877 885 264 272 0 552 184 368 1.332 567 383 .75 1.353 .414 .436 .436
11 3197 1621 78 100 3119 1521 3356 1737 83 104 3278 1637 0 0 1027 443 38 25 100 100 100 100 4640 4915 2.051 .488 .499 .498 .497 1.208 52 301 .484 .98 90 2810 8810 876 885 276 285 0 3073 190 2883 .924 3293 3103 1.082 .947 -.113 -.079 -.079
12 4938 1978 80 102 4858 1876 5269 2109 88 108 5189 2007 0 0 2021 810 43 28 100 100 100 100 6734 7196 2.59 .386 .387 .389 .39 1.269 52 275 .385 .98 80 2960 8810 877 885 292 300 0 3750 193 3556 .732 3998 3805 1.366 .733 -.45 -.448 -.448
13 4595 1664 80 103 4515 1561 4498 1651 83 104 4418 1548 0 0 1648 576 18 14 100 100 100 100 6076 5966 2.892 .346 .35 .342 .341 1.213 80 368 .34 .98 100 3120 8810 876 886 307 317 0 3154 195 2959 .655 3130 2935 1.526 .664 -.61 -.59 -.59
14 329 405 81 101 248 304 320 391 82 103 239 290 0 0 88 105 10 18 100 100 100 100 552 529 .816 1.226 1.213 1.226 1.272 1.294 80 368 1.234 .97 110 3260 8810 875 886 320 331 0 768 191 576 2.324 741 550 .43 2.3 1.216 1.202 1.202
15 706 2301 80 99 626 2202 799 2626 83 102 719 2527 0 0 258 904 37 16 98 100 97 100 2828 3246 .284 3.518 3.515 3.546 3.507 1.285 80 328 3.551 .99 100 3400 8810 876 886 335 345 0 4362 188 4174 6.668 4978 4790 .15 6.663 2.737 2.736 2.736
16 3862 3949 77 97 3785 3852 4027 3996 78 99 3950 3899 0 0 1466 1511 14 12 100 100 100 100 7637 7849 .983 1.018 .987 1.019 1.005 1.224 80 356 1.02 .99 100 3550 8810 876 886 350 360 0 7486 184 7302 1.929 7575 7391 .518 1.871 .948 .904 .904
17 3283 2446 75 97 3208 2349 3320 2561 80 102 3245 2464 0 0 1073 802 40 30 100 100 100 100 5557 5709 1.366 .732 .759 .735 .732 1.238 52 299 .731 .99 90 3690 8810 876 885 364 373 0 4637 184 4453 1.388 4855 4671 .72 1.439 .473 .526 .526
18 256 478 79 99 177 379 262 496 81 109 183 397 0 0 102 207 18 48 100 100 100 91 556 580 .467 2.141 2.169 2.201 2.189 1.438 12 90 2.268 .96 50 3840 8790 876 881 381 386 0 906 188 718 4.059 940 753 .246 4.113 2.021 2.04 2.04
19 4589 4038 76 98 4513 3940 4811 4246 77 99 4735 4148 0 0 1667 1512 10 13 100 100 100 100 8453 8883 1.145 .873 .876 .855 .881 1.301 80 367 .878 .99 100 3990 8810 876 886 394 404 0 7655 186 7469 1.655 8049 7863 .604 1.661 .727 .732 .732
20 3677 2988 75 98 3602 2890 4127 3372 76 99 4052 3274 0 0 1628 1360 10 13 100 100 100 100 6492 7326 1.246 .802 .808 .782 .796 1.354 80 341 .808 .98 100 4130 8810 876 886 408 418 0 5664 186 5479 1.521 6392 6207 .657 1.532 .605 .615 .615

Total number of rows: 43104

Table truncated, full table size 9646 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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