NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM90604 Query DataSets for GSM90604
Status Public on Jan 06, 2006
Title ULL-L-069
Sample type RNA
 
Channel 1
Source name Stratagene Reference, ampl. totRNA
Organism Homo sapiens
Characteristics reference: Stratagene Reference, amplified total RNA
Extracted molecule total RNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name ULL-L-069, ampl. totRNA
Organism Homo sapiens
Characteristics cell type: primary breast carcinoma
ID: ULL-L-069
Extracted molecule total RNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Description Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/35560.gif
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 04, 2006
Last update date Sep 18, 2012
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL3114
Series (2)
GSE3971 Invasive lobular and ductal carcinomas of the breast
GSE40954 TP53 mutation status and gene expression profiles are powerful prognostic markers of breast cancer

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 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
1 1081 381 243 281 838 100 1060 378 245 283 817 97 0 0 495 133 36 45 96 65 90 51 938 914 8.38 .119 .119 1 1 1 52 299 1 .76 80 2240 8430 74 82 66 74 0 693 511 182 .217 687 176 4.609 .216 -2.204 -2.212
2 1883 688 244 272 1639 416 1949 681 247 275 1705 409 0 0 349 96 37 46 100 100 100 100 2055 2114 3.94 .254 .24 1 1 1 32 206 1 .92 70 2380 8420 73 80 80 87 0 1251 495 756 .461 1238 744 2.167 .436 -1.116 -1.197
3 4781 10967 243 264 4538 10703 4993 11122 247 268 4750 10858 0 0 1461 3952 38 47 100 100 100 100 15241 15608 .424 2.359 2.286 1 1 1 80 438 1 .98 100 2530 8420 72 82 94 104 0 19940 480 19460 4.288 20222 19742 .233 4.156 2.1 2.055
4 9882 5387 240 254 9642 5133 9060 5668 248 261 8820 5414 0 0 5450 2489 39 47 100 100 100 100 14775 14234 1.878 .532 .614 1 1 1 32 206 1 .96 70 2670 8430 74 81 109 116 0 9795 462 9333 .968 10305 9844 1.033 1.116 -.047 .158
5 2800 1548 238 248 2562 1300 2425 1537 242 250 2187 1289 0 0 1609 884 34 48 100 100 100 100 3862 3476 1.971 .507 .589 1 1 1 52 290 1 .96 80 2820 8430 74 82 124 132 0 2815 451 2364 .923 2795 2344 1.084 1.072 -.116 .1
6 378 338 233 236 145 102 389 339 236 238 156 103 0 0 108 88 37 41 78 81 71 71 247 259 1.422 .703 .66 1 1 1 32 165 1 .65 60 2960 8420 74 80 139 145 0 615 429 185 1.279 616 187 .782 1.2 .355 .264
7 501 532 231 231 270 301 516 525 233 231 285 294 0 0 107 118 35 39 93 100 93 100 571 579 .897 1.115 1.032 1 1 1 32 225 1 .86 70 3110 8420 73 80 153 160 0 967 420 547 2.027 955 535 .493 1.876 1.019 .907
8 9867 4055 233 237 9634 3818 9513 3764 236 239 9280 3527 0 0 4865 1697 34 42 100 100 100 100 13452 12807 2.523 .396 .38 1 1 1 52 285 1 .98 80 3260 8430 74 82 168 176 0 7373 431 6942 .721 6844 6413 1.388 .691 -.473 -.533
9 4410 4597 231 222 4179 4375 4760 5021 236 231 4529 4799 0 0 1258 1079 65 65 100 100 100 100 8554 9328 .955 1.047 1.06 1 1 1 32 226 1 .98 70 3410 8430 74 81 183 190 0 8358 404 7955 1.903 9129 8725 .525 1.927 .929 .946
10 1105 1951 237 243 868 1708 869 1798 237 249 632 1555 0 0 788 1344 36 43 87 96 84 93 2576 2187 .508 1.968 2.46 1 1 1 32 170 1 .95 60 3560 8440 76 82 199 205 0 3547 442 3105 3.578 3269 2827 .28 4.474 1.839 2.161
11 3709 2617 238 238 3471 2379 2887 1696 238 242 2649 1458 0 0 3089 2218 32 44 100 98 100 94 5850 4107 1.459 .685 .55 1 1 1 52 281 1 .98 80 3700 8440 75 83 212 220 0 4758 433 4325 1.246 3084 2651 .802 1.001 .318 .001
12 3787 2832 238 257 3549 2575 3737 2746 241 258 3499 2489 0 0 1466 1186 39 64 100 100 100 100 6124 5988 1.378 .726 .711 1 1 1 32 219 1 .96 70 3840 8430 74 81 226 233 0 5149 467 4682 1.319 4993 4525 .758 1.293 .4 .371
13 2277 1457 239 256 2038 1201 2295 1493 241 259 2056 1237 0 0 1031 636 37 56 94 96 94 94 3239 3293 1.697 .589 .602 1 1 1 52 335 1 .98 90 3990 8440 74 83 240 249 0 2649 465 2184 1.071 2715 2249 .933 1.094 .1 .13
14 1200 444 239 230 961 214 1184 425 240 233 945 195 0 0 236 108 32 53 100 91 100 83 1175 1140 4.491 .223 .206 1 1 1 12 104 1 .81 50 4140 8430 75 80 257 262 0 807 418 389 .405 773 355 2.47 .375 -1.304 -1.414
15 5148 3990 237 245 4911 3745 5527 4182 241 250 5290 3937 0 0 1581 989 36 49 100 100 100 100 8656 9227 1.311 .763 .744 1 1 1 52 293 1 .98 80 4290 8440 75 83 271 279 0 7255 445 6809 1.386 7604 7158 .721 1.353 .471 .436
16 5200 4389 235 244 4965 4145 5574 4740 247 255 5339 4496 0 0 1508 1504 65 84 100 100 100 100 9110 9835 1.198 .835 .842 1 1 1 32 207 1 .98 70 4420 8420 73 80 284 291 0 7980 444 7536 1.518 8618 8175 .659 1.531 .602 .615
17 918 978 238 259 680 719 953 1042 238 260 715 783 0 0 216 290 35 48 100 96 100 93 1399 1498 .946 1.057 1.095 1 1 1 32 170 1 .96 60 4560 8420 74 80 299 305 0 1778 471 1307 1.922 1895 1424 .52 1.991 .943 .994
18 298 173 238 264 60 -91 253 166 240 265 15 -98 0 0 106 54 35 45 46 0 46 0 -31 -83 null null null 1 1 1 52 275 1 .05 80 4710 8430 74 82 313 321 0 315 480 -165 null 302 null null null null null
19 2380 904 242 271 2138 633 2345 888 245 270 2103 617 0 0 613 226 35 41 100 100 100 100 2771 2720 3.378 .296 .293 1 1 1 52 332 1 .95 90 4860 8440 74 83 327 336 0 1644 493 1151 .538 1615 1122 1.858 .533 -.893 -.907
20 660 610 245 269 415 341 746 679 244 273 501 410 0 0 221 211 33 46 90 90 87 78 756 911 1.217 .822 .818 1 1 1 32 171 1 .91 60 5000 8430 75 81 343 349 0 1109 489 620 1.494 1235 745 .669 1.488 .579 .573

Total number of rows: 43008

Table truncated, full table size 9049 Kbytes.




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