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Sample GSM90559 Query DataSets for GSM90559
Status Public on Jan 06, 2006
Title ULL-L-097
Sample type RNA
 
Channel 1
Source name Stratagene_aT
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-097_aT
Organism Homo sapiens
Characteristics cell type: primary breast carcinoma
ID: ULL-L-097
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/2002-01/24805.gif
Scanner Make: Axon
name: 24805_Scanner Make
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 GPL2790
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 1977 1685 180 180 1797 1505 1948 1638 184 186 1768 1458 0 0 413 393 33 47 100 100 100 100 3302 3226 1.194 .838 .825 .834 .85 1.211 52 325 .823 .97 90 2020 7540 45 54 61 70 0 1755 188 1568 .872 1706 1519 1.146 .859 -.197 -.219
2 2287 1385 185 180 2102 1205 2396 1352 186 184 2211 1172 0 0 689 405 32 43 100 100 100 100 3307 3383 1.744 .573 .53 .571 .56 1.197 80 303 .561 .97 100 2170 7550 46 56 76 86 0 1443 188 1255 .597 1408 1221 1.675 .552 -.744 -.857
3 4990 15690 190 188 4800 15502 5056 16437 194 188 4866 16249 0 0 1423 4104 35 38 100 100 100 100 20302 21115 .31 3.23 3.339 3.27 3.325 1.266 120 400 3.279 .96 120 2310 7550 45 57 89 101 0 16344 196 16148 3.364 17122 16926 .297 3.478 1.75 1.798
4 16110 29383 214 204 15896 29179 14952 27306 213 207 14738 27102 0 0 7596 13980 40 41 100 100 100 100 45075 41840 .545 1.836 1.839 1.843 1.845 1.278 80 321 1.855 .98 100 2460 7550 46 56 105 115 0 30607 213 30395 1.912 28444 28231 .523 1.916 .935 .938
5 3316 2957 219 211 3097 2746 3397 3207 222 212 3178 2996 0 0 1541 1361 39 45 100 100 100 100 5843 6174 1.128 .887 .943 .892 .905 1.236 52 236 .881 .98 80 2610 7540 46 54 121 129 0 3080 220 2860 .924 3341 3121 1.083 .982 -.115 -.026
6 1374 1264 213 204 1161 1060 1442 1335 218 213 1229 1131 0 0 444 429 49 83 100 100 98 98 2221 2360 1.095 .913 .92 .908 .923 1.386 80 357 .918 .97 100 2760 7540 45 55 135 145 0 1317 213 1104 .951 1391 1178 1.051 .959 -.072 -.061
7 1461 2012 206 193 1255 1819 1473 2140 216 217 1267 1947 0 0 306 511 65 140 100 100 100 100 3074 3214 .69 1.449 1.537 1.42 1.472 1.219 52 266 1.474 .98 90 2890 7530 44 53 148 157 0 2096 201 1895 1.51 2229 2028 .662 1.601 .594 .679
8 10489 15421 204 189 10285 15232 10948 15500 209 200 10744 15311 0 0 3597 5382 51 100 100 100 100 100 25517 26055 .675 1.481 1.425 1.479 1.476 1.242 80 354 1.489 .98 100 3040 7550 46 56 163 173 0 16064 197 15867 1.543 16146 15949 .648 1.484 .625 .57
9 3742 5571 199 179 3543 5392 3923 5312 203 185 3724 5133 0 0 1269 1955 37 51 100 100 100 100 8935 8857 .657 1.522 1.378 1.534 1.488 1.253 80 337 1.523 .98 100 3190 7550 46 56 178 188 0 5803 186 5617 1.585 5533 5347 .631 1.436 .665 .522
10 1623 4717 199 180 1424 4537 1674 4893 203 200 1475 4713 0 0 427 1400 35 99 100 100 100 100 5961 6188 .314 3.186 3.195 3.183 3.15 1.209 52 251 3.291 .97 90 3330 7540 45 54 192 201 0 4914 188 4726 3.319 5097 4909 .301 3.328 1.731 1.735
11 8775 5330 207 193 8568 5137 9244 5535 214 211 9037 5342 0 0 2601 1837 83 132 100 100 100 100 13705 14379 1.668 .6 .591 .584 .611 1.255 120 406 .605 .98 120 3480 7550 45 57 206 218 0 5552 201 5351 .625 5766 5565 1.601 .616 -.679 -.7
12 4354 1963 199 180 4155 1783 4419 2001 201 187 4220 1821 0 0 1315 560 36 37 100 100 100 100 5938 6041 2.33 .429 .432 .428 .424 1.21 80 270 .417 .98 100 3630 7550 46 56 222 232 0 2045 188 1857 .447 2084 1897 2.237 .449 -1.162 -1.154
13 3637 3138 185 175 3452 2963 3617 3061 189 178 3432 2886 0 0 1250 1054 33 38 100 100 100 100 6415 6318 1.165 .858 .841 .869 .877 1.25 80 300 .847 .97 100 3770 7550 46 56 236 246 0 3269 182 3086 .894 3189 3006 1.118 .876 -.161 -.191
14 1005 738 188 173 817 565 1015 712 191 178 827 539 0 0 277 229 34 39 100 100 100 100 1382 1366 1.446 .692 .652 .675 .676 1.356 80 345 .702 .95 100 3920 7550 46 56 251 261 0 769 180 589 .72 742 561 1.388 .679 -.473 -.559
15 9275 9167 201 182 9074 8985 9845 9689 203 184 9644 9507 0 0 2109 2009 33 39 100 100 100 100 18059 19151 1.01 .99 .986 .988 .986 1.169 80 371 .982 .98 110 4070 7550 45 56 265 276 0 9549 190 9359 1.031 10093 9903 .97 1.027 .045 .038
16 8253 10579 200 172 8053 10407 8882 10801 201 177 8682 10629 0 0 1957 2709 36 41 100 100 100 100 18460 19311 .774 1.292 1.224 1.287 1.302 1.175 80 316 1.312 .98 100 4210 7550 46 56 280 290 0 11020 179 10841 1.346 11251 11072 .743 1.275 .429 .351
17 1090 2601 202 180 888 2421 1125 2717 205 183 923 2537 0 0 309 767 37 39 100 100 100 100 3309 3460 .367 2.726 2.749 2.758 2.748 1.203 80 334 2.732 .98 100 4360 7550 46 56 295 305 0 2709 188 2522 2.84 2830 2643 .352 2.863 1.506 1.518
18 740 662 209 186 531 476 774 655 214 190 565 469 0 0 153 154 37 40 100 100 100 100 1007 1034 1.116 .896 .83 .891 .88 1.261 52 259 .908 .95 90 4500 7550 46 55 309 318 0 690 194 496 .934 682 489 1.071 .865 -.099 -.21
19 3322 3150 216 193 3106 2957 3409 3358 219 195 3193 3165 0 0 743 846 36 40 100 100 100 100 6063 6358 1.05 .952 .991 .926 .963 1.247 120 414 .969 .98 120 4650 7550 45 57 323 335 0 3281 201 3080 .992 3498 3297 1.008 1.033 -.012 .046
20 1176 2971 221 199 955 2772 1234 2964 225 198 1013 2765 0 0 303 1024 37 36 100 100 100 100 3727 3778 .345 2.903 2.73 2.79 2.934 1.279 80 264 3.055 .97 100 4800 7550 46 56 339 349 0 3095 207 2888 3.024 3088 2880 .331 2.843 1.596 1.508

Total number of rows: 43008

Table truncated, full table size 9832 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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