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Sample GSM79863 Query DataSets for GSM79863
Status Public on Oct 25, 2005
Title HCC (HBV+, HK3)
Sample type RNA
 
Channel 1
Source name Liver Reference 1
Organism Homo sapiens
Characteristics Liver Reference 1
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name HCC (HBV+, HK3)
Organism Homo sapiens
Characteristics HCC (HBV+, HK3)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Liver
Image: http://smd.stanford.edu/MicroArray/gifs/2000-07/7442.gif
Data processing LOG_RAT2N_MEDIAN is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Oct 24, 2005
Last update date Sep 22, 2006
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 GPL2948
Series (1)
GSE3500 Gene expression patterns in human liver cancers

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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 856 674 54 49 802 625 null null 57 51 null null null null null null null null 100 100 null null null null 1.283 .779 null null .786 null 80 422 .742 .93 null null null 66 76 68 78 0 601 43 558 .696 null null 1.437 null -.523 null
2 574 300 53 46 521 254 null null 55 48 null null null null null null null null 100 100 null null null null 2.051 .488 null null .507 null 52 289 .439 .92 null null null 66 75 83 92 0 267 41 226 .434 null null 2.305 null -1.205 null
3 355 222 52 45 303 177 null null 54 47 null null null null null null null null 100 100 null null null null 1.712 .584 null null .539 null 80 353 .519 .9 null null null 67 77 98 108 0 198 40 158 .521 null null 1.918 null -.939 null
4 148 422 51 43 97 379 null null 55 47 null null null null null null null null 98 100 null null null null .256 3.907 null null 3.94 null 80 398 2.879 .82 null null null 66 77 112 123 0 376 38 338 3.485 null null .287 null 1.801 null
5 1333 157 50 42 1283 115 null null 54 45 null null null null null null null null 100 100 null null null null 11.157 .09 null null .085 null 80 405 .081 .84 null null null 65 76 128 139 0 140 37 103 .08 null null 12.456 null -3.639 null
6 877 493 50 43 827 450 null null 54 46 null null null null null null null null 100 100 null null null null 1.838 .544 null null .549 null 80 368 .52 .95 null null null 66 76 144 154 0 440 38 402 .486 null null 2.057 null -1.041 null
7 288 207 51 43 237 164 null null 53 46 null null null null null null null null 100 100 null null null null 1.445 .692 null null .666 null 52 276 .585 .88 null null null 67 75 160 168 0 184 38 146 .616 null null 1.623 null -.699 null
8 199 427 50 41 149 386 null null 52 44 null null null null null null null null 96 100 null null null null .386 2.591 null null 2.553 null 52 242 2.005 .88 null null null 68 76 176 184 0 381 36 345 2.315 null null .432 null 1.211 null
9 5875 2206 51 44 5824 2162 null null 53 46 null null null null null null null null 100 98 null null null null 2.694 .371 null null .373 null 80 341 .365 .96 null null null 66 76 188 198 0 1969 39 1930 .331 null null 3.018 null -1.593 null
10 914 2961 51 47 863 2914 null null 56 47 null null null null null null null null 96 100 null null null null .296 3.377 null null 3.404 null 80 342 3.058 .95 null null null 67 77 203 213 0 2643 41 2602 3.015 null null .332 null 1.592 null
11 456 700 52 47 404 653 null null 53 49 null null null null null null null null 100 100 null null null null .619 1.616 null null 1.58 null 52 294 1.556 .95 null null null 66 75 217 226 0 625 41 584 1.446 null null .692 null .532 null
12 1063 306 54 47 1009 259 null null 59 52 null null null null null null null null 100 96 null null null null 3.896 .257 null null .249 null 80 393 .248 .95 null null null 67 77 233 243 0 273 41 232 .23 null null 4.349 null -2.121 null
13 670 310 57 47 613 263 null null 66 56 null null null null null null null null 98 98 null null null null 2.331 .429 null null .441 null 80 347 .405 .95 null null null 67 77 248 258 0 276 41 235 .383 null null 2.609 null -1.383 null
14 6470 3015 57 45 6413 2970 null null 63 49 null null null null null null null null 100 100 null null null null 2.159 .463 null null .464 null 80 406 .453 .96 null null null 66 77 261 272 0 2691 40 2651 .413 null null 2.419 null -1.274 null
15 313 223 57 45 256 178 null null 62 47 null null null null null null null null 96 100 null null null null 1.438 .695 null null .666 null 80 343 .606 .91 null null null 68 78 277 287 0 199 40 159 .621 null null 1.61 null -.687 null
16 724 522 59 46 665 476 null null 63 49 null null null null null null null null 100 97 null null null null 1.397 .716 null null .733 null 80 351 .694 .95 null null null 67 77 292 302 0 466 41 425 .639 null null 1.565 null -.646 null
17 4529 3843 63 50 4466 3793 null null 66 53 null null null null null null null null 100 100 null null null null 1.177 .849 null null .838 null 80 390 .807 .97 null null null 68 78 307 317 0 3431 44 3387 .758 null null 1.319 null -.399 null
18 232 428 65 49 167 379 null null 66 51 null null null null null null null null 96 100 null null null null .441 2.269 null null 2.193 null 32 164 2.152 .88 null null null 70 76 325 331 0 382 43 339 2.03 null null .493 null 1.021 null
19 2512 3247 60 46 2452 3201 null null 62 49 null null null null null null null null 100 100 null null null null .766 1.305 null null 1.318 null 52 318 1.244 .96 null null null 68 77 336 345 0 2899 41 2858 1.166 null null .858 null .221 null
20 530 693 60 47 470 646 null null 62 49 null null null null null null null null 100 100 null null null null .728 1.374 null null 1.384 null 52 324 1.28 .94 null null null 68 77 351 360 0 618 41 577 1.228 null null .815 null .296 null

Total number of rows: 24192

Table truncated, full table size 5651 Kbytes.




Supplementary data files not provided
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