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Sample GSM90992 Query DataSets for GSM90992
Status Public on Aug 13, 2007
Title BC-M-298
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-298
Organism Homo sapiens
Characteristics BC-M-298
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-02/49778.gif; format: GIF
Datafile type: GenePix Results 3
name: 49778_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
1 362 198 86 90 276 108 361 190 88 93 275 100 0 0 95 48 12 13 100 100 100 96 384 375 2.556 .391 .364 .379 .393 1.555 32 204 .378 .9 70 1470 8600 856 863 143 150 0 491 223 268 .971 472 248 1.03 .902 -.042 -.148 -.148
2 13004 1221 87 91 12917 1130 14803 1307 88 93 14716 1216 0 0 6422 558 12 10 100 100 100 100 14047 15932 11.431 .087 .083 .087 .086 1.391 52 329 .086 .99 90 1610 8590 854 863 156 165 0 3030 226 2804 .217 3244 3018 4.606 .205 -2.204 -2.286 -2.286
3 1876 977 85 97 1791 880 1431 777 86 99 1346 680 0 0 1265 645 11 16 100 100 100 100 2671 2026 2.035 .491 .505 .459 .475 1.358 32 170 .491 .98 60 1760 8580 855 861 173 179 0 2425 241 2184 1.219 1928 1688 .82 1.254 .286 .326 .326
4 1550 346 88 101 1462 245 1629 333 89 102 1541 232 0 0 562 110 12 15 100 100 100 100 1707 1773 5.967 .168 .151 .164 .173 1.279 32 214 .167 .96 70 1900 8590 855 862 186 193 0 859 251 608 .416 826 576 2.404 .374 -1.266 -1.42 -1.42
5 10846 4482 88 96 10758 4386 10770 4377 89 98 10682 4281 0 0 4942 1967 12 12 100 100 100 100 15144 14963 2.453 .408 .401 .419 .394 1.351 52 284 .401 .98 80 2050 8590 855 863 201 209 0 11123 238 10885 1.012 10863 10624 .988 .995 .017 -.008 -.008
6 590 283 86 94 504 189 589 262 87 95 503 168 0 0 158 70 11 11 100 100 100 100 693 671 2.667 .375 .334 .373 .37 1.327 32 212 .364 .94 70 2200 8590 855 862 216 223 0 702 233 469 .931 650 417 1.075 .829 -.104 -.271 -.271
7 5621 2377 85 95 5536 2282 5239 2190 86 95 5154 2095 0 0 3489 1391 11 10 100 100 100 100 7818 7249 2.426 .412 .406 .438 .439 1.425 52 276 .4 .97 80 2350 8590 855 863 231 239 0 5899 236 5663 1.023 5435 5199 .978 1.009 .033 .013 .013
8 648 805 85 96 563 709 612 782 90 97 527 686 0 0 166 242 39 18 100 100 100 100 1272 1213 .794 1.259 1.302 1.239 1.27 1.202 32 213 1.271 .97 70 2490 8590 855 862 245 252 0 1998 238 1760 3.125 1941 1702 .32 3.231 1.644 1.692 1.692
9 2834 542 87 97 2747 445 2749 504 89 99 2662 407 0 0 678 158 17 21 100 100 100 100 3192 3069 6.173 .162 .153 .157 .156 1.328 52 328 .16 .95 90 2640 8590 854 863 259 268 0 1345 241 1104 .402 1251 1010 2.487 .379 -1.315 -1.398 -1.398
10 770 175 85 99 685 76 695 165 86 99 610 66 0 0 295 38 10 10 100 100 100 96 761 676 9.013 .111 .108 .106 .114 1.577 32 206 .098 .84 70 2780 8590 855 862 274 281 0 434 246 189 .275 409 164 3.632 .269 -1.861 -1.897 -1.897
11 7353 6535 84 97 7269 6438 7184 6734 85 97 7100 6637 0 0 2210 2217 11 11 100 100 100 100 13707 13737 1.129 .886 .935 .871 .898 1.264 52 294 .897 .98 80 2930 8590 855 863 289 297 0 16218 241 15977 2.198 16712 16471 .455 2.32 1.136 1.214 1.214
12 11335 4522 86 95 11249 4427 11236 4532 90 98 11150 4437 0 0 5337 2177 17 16 100 100 100 100 15676 15587 2.541 .394 .398 .388 .41 1.329 32 212 .39 .98 70 3080 8590 855 862 304 311 0 11222 236 10987 .977 11247 11011 1.024 .988 -.034 -.018 -.018
13 14200 6006 89 98 14111 5908 14163 5526 91 101 14074 5428 0 0 7217 3612 14 15 100 100 100 100 20019 19502 2.388 .419 .386 .378 .403 1.376 52 316 .434 .98 90 3220 8590 854 863 317 326 0 14905 243 14662 1.039 13714 13471 .962 .957 .055 -.063 -.063
14 713 438 84 95 629 343 712 422 85 96 628 327 0 0 208 150 10 12 100 100 100 100 972 955 1.834 .545 .521 .53 .525 1.301 52 312 .555 .96 90 3360 8590 854 863 331 340 0 1087 236 851 1.353 1047 812 .739 1.292 .437 .37 .37
15 827 6961 81 94 746 6867 825 6905 82 95 744 6811 0 0 160 1611 10 11 100 100 100 100 7613 7555 .109 9.205 9.155 9.19 9.346 1.16 52 324 9.376 .98 90 3510 8590 854 863 346 355 0 17275 233 17042 22.845 17136 16903 .044 22.719 4.514 4.506 4.506
16 8033 6573 80 95 7953 6478 8088 6685 81 96 8008 6590 0 0 2236 1952 10 12 100 100 100 100 14431 14598 1.228 .815 .823 .812 .828 1.17 52 324 .817 .99 90 3660 8590 854 863 361 370 0 16313 236 16077 2.021 16590 16355 .495 2.042 1.015 1.03 1.03
17 6551 4632 78 95 6473 4537 6898 4884 80 96 6820 4789 0 0 3067 2254 11 11 100 100 100 100 11010 11609 1.427 .701 .702 .691 .709 1.393 52 264 .705 .99 80 3800 8590 855 863 376 384 0 11495 236 11260 1.739 12121 11885 .575 1.743 .799 .801 .801
18 127 154 77 93 50 61 86 104 79 94 9 11 0 0 113 127 11 11 42 48 25 30 111 20 .82 1.22 1.222 1.16 1.42 2.436 52 264 1.162 .87 80 3950 8580 854 862 391 399 -50 382 231 151 3.028 258 27 .33 3.033 1.598 1.601
19 11425 7351 79 94 11346 7257 12299 7755 80 94 12220 7661 0 0 3418 2535 10 10 100 100 100 100 18603 19881 1.563 .64 .627 .63 .637 1.229 52 301 .647 .99 90 4090 8590 854 863 404 413 0 18243 233 18010 1.587 19246 19013 .63 1.556 .667 .638 .638
20 11318 6151 82 96 11236 6055 11157 5889 175 156 11075 5793 0 0 3762 2110 635 404 100 100 100 100 17291 16868 1.856 .539 .523 .537 .536 1.209 52 264 .538 .99 80 4240 8590 855 863 420 428 0 15265 238 15027 1.337 14615 14377 .748 1.298 .419 .376 .376

Total number of rows: 43104

Table truncated, full table size 9871 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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