NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM90974 Query DataSets for GSM90974
Status Public on Aug 13, 2007
Title BC-M-057
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-057
Organism Homo sapiens
Characteristics BC-M-057
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Breast
Image: http://smd.stanford.edu/MicroArray/gifs/2004-04/50740.gif; format: GIF
Datafile type: GenePix Results 3
name: 50740_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
1 425 565 169 115 256 450 444 594 171 116 275 479 0 0 53 117 26 17 100 100 100 100 706 754 .569 1.758 1.742 1.723 1.765 1.212 52 337 1.794 .96 90 1390 4360 431 440 134 143 0 1069 218 852 3.327 1124 907 .301 3.297 1.734 1.721 1.721
2 9094 3061 156 113 8938 2948 9833 3466 202 127 9677 3353 0 0 4507 1600 681 220 100 98 98 95 11886 13030 3.032 .33 .346 .314 .336 1.197 80 414 .333 .99 110 1550 4370 431 442 149 160 0 5794 214 5580 .624 6561 6347 1.602 .656 -.68 -.609 -.609
3 5181 2324 150 116 5031 2208 5711 2485 276 238 5561 2369 0 0 1691 846 748 806 100 92 96 73 7239 7930 2.279 .439 .426 .427 .44 1.171 52 288 .448 .99 90 1690 4360 431 440 164 173 0 4399 220 4179 .831 4704 4484 1.204 .806 -.268 -.311 -.311
4 1632 183 150 115 1482 68 1647 184 252 217 1497 69 0 0 719 42 683 736 85 0 52 0 1550 1566 21.794 .046 .046 .043 .046 1.518 80 346 .06 .56 100 1840 4360 431 441 179 189 0 346 218 129 .087 348 131 11.514 .087 -3.525 -3.519 -3.519
5 1284 2510 148 113 1136 2397 1376 2750 153 118 1228 2637 0 0 275 637 26 39 100 100 100 100 3533 3865 .474 2.11 2.147 2.088 2.095 1.105 52 286 2.154 .99 90 1970 4360 431 440 192 201 0 4751 214 4537 3.994 5205 4991 .25 4.065 1.998 2.023 2.023
6 514 211 149 114 365 97 514 211 151 119 365 97 0 0 113 42 18 37 100 98 100 75 462 462 3.763 .266 .266 .256 .263 1.31 52 324 .258 .9 90 2120 4360 431 440 207 216 0 399 216 184 .503 399 184 1.988 .503 -.991 -.991 -.991
7 1215 1250 147 113 1068 1137 1342 1427 148 114 1195 1314 0 0 419 430 12 12 100 100 100 100 2205 2509 .939 1.065 1.1 1.075 1.064 1.214 52 254 1.062 .99 80 2270 4360 432 440 223 231 0 2366 214 2152 2.015 2701 2487 .496 2.081 1.011 1.058 1.058
8 732 324 143 112 589 212 785 320 143 113 642 208 0 0 151 61 11 11 100 100 100 100 801 850 2.778 .36 .324 .357 .36 1.247 80 349 .355 .96 100 2420 4360 431 441 237 247 0 613 212 401 .681 606 394 1.468 .613 -.554 -.705 -.705
9 909 229 139 113 770 116 934 233 140 114 795 120 0 0 156 35 17 13 100 100 100 100 886 915 6.638 .151 .151 .146 .15 1.257 80 317 .15 .95 100 2570 4360 431 441 252 262 0 433 214 220 .285 441 227 3.507 .286 -1.81 -1.807 -1.807
10 884 841 142 117 742 724 908 833 143 118 766 716 0 0 180 201 18 13 100 100 100 100 1466 1482 1.025 .976 .935 .965 .988 1.155 80 309 .991 .98 100 2710 4360 431 441 266 276 0 1592 221 1370 1.847 1577 1355 .541 1.769 .885 .823 .823
11 4807 3239 143 118 4664 3121 4968 3388 145 119 4825 3270 0 0 1139 887 20 13 100 100 100 100 7785 8095 1.494 .669 .678 .657 .671 1.14 80 376 .681 .99 110 2860 4360 430 441 280 291 0 6131 223 5908 1.267 6413 6190 .789 1.283 .341 .359 .359
12 3319 6193 144 116 3175 6077 3517 6569 146 118 3373 6453 0 0 1139 2272 15 11 100 100 100 100 9252 9826 .522 1.914 1.913 1.876 1.94 1.311 80 344 1.939 .99 100 3000 4360 431 441 295 305 0 11722 220 11503 3.623 12434 12215 .276 3.621 1.857 1.857 1.857
13 3389 1733 141 115 3248 1618 3638 1792 166 126 3497 1677 0 0 729 422 133 66 100 100 100 100 4866 5174 2.007 .498 .48 .49 .495 1.158 52 289 .5 .99 90 3140 4360 431 440 309 318 0 3280 218 3063 .943 3392 3174 1.061 .908 -.085 -.14 -.14
14 361 465 135 113 226 352 359 464 153 121 224 351 0 0 32 75 119 59 100 100 36 98 578 575 .642 1.558 1.567 1.532 1.543 1.188 80 371 1.238 .83 100 3300 4360 431 441 325 335 0 880 214 666 2.948 878 664 .339 2.966 1.56 1.569 1.569
15 518 2631 133 113 385 2518 529 2766 135 113 396 2653 0 0 90 609 17 11 100 100 100 100 2903 3049 .153 6.54 6.699 6.508 6.606 1.161 80 314 6.721 .98 100 3450 4360 431 441 340 350 0 4980 214 4766 12.38 5236 5022 .081 12.681 3.63 3.665 3.665
16 5606 3090 132 110 5474 2980 5685 3163 135 111 5553 3053 0 0 830 581 19 11 100 100 100 100 8454 8606 1.837 .544 .55 .539 .548 1.113 80 337 .548 .99 100 3590 4360 431 441 354 364 0 5849 208 5641 1.03 5987 5779 .97 1.041 .043 .058 .058
17 4459 3061 127 112 4332 2949 4766 3195 129 112 4639 3083 0 0 1190 824 17 11 100 100 100 100 7281 7722 1.469 .681 .665 .681 .678 1.173 80 340 .68 .99 100 3740 4360 431 441 369 379 0 5794 212 5582 1.289 6048 5836 .776 1.258 .366 .331 .331
18 1517 639 121 108 1396 531 1610 649 122 108 1489 541 0 0 332 117 10 10 100 100 100 100 1927 2030 2.629 .38 .363 .387 .385 1.203 80 309 .372 .98 100 3880 4360 431 441 383 393 0 1210 204 1005 .72 1228 1024 1.389 .688 -.474 -.54 -.54
19 4106 2563 119 106 3987 2457 4431 2817 122 107 4312 2711 0 0 1266 783 35 16 100 100 100 100 6444 7023 1.623 .616 .629 .616 .608 1.175 80 319 .615 .99 100 4030 4360 431 441 398 408 0 4851 201 4651 1.166 5332 5132 .857 1.19 .222 .251 .251
20 6819 2169 122 107 6697 2062 7507 2346 126 109 7385 2239 0 0 2438 764 36 18 100 100 100 100 8759 9624 3.248 .308 .303 .307 .311 1.212 80 328 .307 .99 100 4170 4360 431 441 412 422 0 4106 203 3903 .583 4441 4238 1.716 .574 -.779 -.801 -.801

Total number of rows: 43200

Table truncated, full table size 9919 Kbytes.




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