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Sample GSM90608 Query DataSets for GSM90608
Status Public on Jan 06, 2006
Title ULL-L-105
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-105, ampl. totRNA
Organism Homo sapiens
Characteristics cell type: primary breast carcinoma
ID: ULL-L-105
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/2002-11/35566.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 1364 510 295 300 1069 210 1337 475 299 298 1042 175 0 0 402 150 35 50 100 90 100 76 1279 1217 5.09 .196 .168 1 1 1 52 289 1 .84 80 2270 8330 101 109 71 79 0 1186 698 488 .457 1105 407 2.189 .391 -1.13 -1.356
2 1536 304 301 296 1235 8 1472 302 303 296 1171 6 0 0 468 66 34 53 100 28 100 3 1243 1177 154.375 .006 .005 1 1 1 52 256 1 .3 80 2420 8320 100 108 86 94 0 707 688 19 .015 702 14 66.381 .012 -6.053 -6.391
3 5246 15644 297 286 4949 15358 5803 17059 298 290 5506 16773 0 0 1840 5972 39 54 100 100 100 100 20307 22279 .322 3.103 3.046 1 1 1 80 396 1 1 100 2560 8310 98 108 99 109 0 36381 665 35716 7.217 39672 39007 .139 7.084 2.851 2.825
4 9754 7413 298 284 9456 7129 8226 6246 300 288 7928 5962 0 0 5355 4285 39 54 100 100 100 100 16585 13890 1.326 .754 .752 1 1 1 52 268 1 .99 80 2710 8310 99 107 115 123 0 17240 660 16579 1.753 14526 13865 .57 1.749 .81 .806
5 3615 1487 292 262 3323 1225 3736 1492 296 270 3444 1230 0 0 1132 470 77 58 100 100 100 100 4548 4674 2.713 .369 .357 1 1 1 32 213 1 .98 70 2850 8310 99 106 129 136 0 3458 609 2849 .857 3470 2860 1.166 .831 -.222 -.268
6 364 219 293 294 71 -75 345 216 293 295 52 -78 0 0 103 46 37 56 57 1 46 0 -4 -26 null null null 1 1 1 52 305 1 .05 80 3000 8320 100 108 144 152 0 509 684 -174 null 502 null null null null null
7 658 641 301 307 357 334 628 674 310 315 327 367 0 0 105 154 55 75 100 100 100 83 691 694 1.069 .936 1.122 1 1 1 12 90 1 .83 50 3150 8300 99 104 160 165 0 1491 714 777 2.176 1567 853 .46 2.61 1.122 1.384
8 9652 6429 298 306 9354 6123 10452 6756 300 308 10154 6450 0 0 3998 2601 37 58 100 100 100 100 15477 16604 1.528 .655 .635 1 1 1 52 262 1 .99 80 3300 8310 99 107 174 182 0 14951 712 14240 1.522 15712 15000 .657 1.477 .606 .563
9 4192 2759 301 307 3891 2452 4135 2655 302 309 3834 2348 0 0 1012 737 37 52 100 100 100 100 6343 6182 1.587 .63 .612 1 1 1 52 268 1 .99 80 3440 8320 100 108 188 196 0 6416 714 5702 1.466 6174 5460 .682 1.424 .551 .51
10 1738 1099 303 307 1435 792 1729 1087 304 312 1426 780 0 0 701 421 38 52 100 90 96 90 2227 2206 1.812 .552 .547 1 1 1 32 170 1 .97 60 3590 8320 101 107 204 210 0 2556 714 1842 1.284 2528 1814 .779 1.272 .36 .347
11 6406 2377 308 318 6098 2059 6307 2098 306 320 5999 1780 0 0 3812 1604 36 55 100 100 100 98 8157 7779 2.962 .338 .297 1 1 1 52 264 1 .99 80 3740 8320 100 108 218 226 0 5528 740 4788 .785 4879 4140 1.274 .69 -.349 -.535
12 3734 1028 305 335 3429 693 3550 909 306 338 3245 574 0 0 1964 554 38 57 100 94 100 94 4122 3819 4.948 .202 .177 1 1 1 52 267 1 .96 80 3880 8320 100 108 232 240 0 2391 779 1612 .47 2114 1335 2.128 .411 -1.089 -1.282
13 2951 1190 312 342 2639 848 2899 1170 311 344 2587 828 0 0 972 391 35 53 100 100 100 100 3487 3415 3.112 .321 .32 1 1 1 52 243 1 .98 80 4030 8320 100 108 247 255 0 2767 795 1972 .747 2721 1926 1.338 .744 -.42 -.426
14 687 258 312 350 375 -92 529 234 312 355 217 -116 0 0 407 100 37 64 65 7 61 1 283 101 null null null 1 1 1 52 256 1 .18 80 4170 8310 99 107 261 269 0 600 814 -214 null 544 null null null null null
15 7491 2761 313 356 7178 2405 7383 2654 316 365 7070 2298 0 0 2076 831 47 71 100 100 100 100 9583 9368 2.985 .335 .325 1 1 1 52 290 1 .99 90 4320 8320 99 108 275 284 0 6421 828 5593 .779 6172 5344 1.283 .756 -.36 -.404
16 5480 3445 309 354 5171 3091 5786 3578 311 356 5477 3224 0 0 1565 1041 38 65 100 100 100 98 8262 8701 1.673 .598 .589 1 1 1 52 258 1 .99 80 4450 8310 99 107 289 297 0 8012 823 7188 1.39 8321 7498 .719 1.369 .475 .453
17 1293 695 319 356 974 339 1283 693 318 355 964 337 0 0 124 110 45 65 100 100 100 100 1313 1301 2.873 .348 .35 1 1 1 32 224 1 .9 70 4590 8310 99 106 303 310 0 1616 828 788 .809 1612 784 1.235 .813 -.305 -.299
18 378 226 318 362 60 -136 346 207 318 361 28 -155 0 0 117 104 42 60 48 5 40 5 -76 -127 null null null 1 1 1 52 274 1 .03 80 4750 8310 99 107 319 327 0 526 842 -316 null 481 null null null null null
19 3892 1708 321 360 3571 1348 4089 1674 324 362 3768 1314 0 0 947 451 46 61 100 100 100 100 4919 5082 2.649 .377 .349 1 1 1 52 330 1 .98 90 4890 8300 97 106 332 341 0 3972 837 3135 .878 3893 3056 1.139 .811 -.188 -.302
20 1029 512 313 348 716 164 1033 508 321 343 720 160 0 0 90 79 46 63 100 100 100 58 880 880 4.366 .229 .222 1 1 1 12 98 1 .81 50 5030 8300 99 104 348 353 0 1191 809 381 .533 1181 372 1.877 .517 -.909 -.952

Total number of rows: 43008

Table truncated, full table size 9212 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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