NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM79983 Query DataSets for GSM79983
Status Public on Oct 25, 2005
Title HCC (HBV+, HK31)
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+, HK31)
Organism Homo sapiens
Characteristics HCC (HBV+, HK31)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tumor, Liver
Image: http://smd.stanford.edu/MicroArray/gifs//7344.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
1 407 349 62 44 345 305 null null 64 45 null null null null null null null null 100 100 null null null null 1.131 .884 null null .89 null 80 406 .819 .93 null null null 38 48 143 153 0 383 48 335 .971 null null 1.03 null -.042 null
2 269 188 62 42 207 146 null null 63 44 null null null null null null null null 96 96 null null null null 1.418 .705 null null .696 null 80 323 .605 .89 null null null 38 48 158 168 0 206 46 160 .773 null null 1.294 null -.372 null
3 179 142 63 43 116 99 null null 63 44 null null null null null null null null 100 100 null null null null 1.172 .853 null null .785 null 80 305 .652 .84 null null null 39 49 172 182 0 156 47 109 .94 null null 1.064 null -.09 null
4 106 83 63 43 43 40 null null 64 44 null null null null null null null null 89 85 null null null null 1.075 .93 null null .98 null 120 503 .531 .59 null null null 36 49 185 198 0 91 47 44 1.023 null null .977 null .033 null
5 555 289 66 42 489 247 null null 67 44 null null null null null null null null 100 100 null null null null 1.98 .505 null null .49 null 80 305 .452 .92 null null null 39 49 203 213 0 317 46 271 .554 null null 1.804 null -.852 null
6 455 288 64 43 391 245 null null 65 45 null null null null null null null null 100 100 null null null null 1.596 .627 null null .628 null 80 361 .567 .93 null null null 39 49 217 227 0 316 47 269 .688 null null 1.454 null -.54 null
7 171 123 60 42 111 81 null null 62 44 null null null null null null null null 100 100 null null null null 1.37 .73 null null .776 null 52 282 .615 .8 null null null 39 47 233 241 0 135 46 89 .802 null null 1.247 null -.319 null
8 117 168 60 43 57 125 null null 62 44 null null null null null null null null 94 100 null null null null .456 2.193 null null 2.133 null 52 242 1.518 .8 null null null 41 49 249 257 0 184 47 137 2.404 null null .416 null 1.265 null
9 4881 505 60 45 4821 460 null null 63 48 null null null null null null null null 100 100 null null null null 10.48 .095 null null .095 null 80 357 .09 .95 null null null 39 49 262 272 0 554 49 505 .105 null null 9.547 null -3.255 null
10 676 3837 62 43 614 3794 null null 63 46 null null null null null null null null 100 100 null null null null .162 6.179 null null 6.299 null 52 292 5.817 .96 null null null 39 48 276 285 0 4216 47 4169 6.79 null null .147 null 2.763 null
11 293 196 61 43 232 153 null null 63 45 null null null null null null null null 100 100 null null null null 1.516 .659 null null .651 null 52 288 .571 .87 null null null 40 48 292 300 0 215 47 168 .724 null null 1.381 null -.466 null
12 596 149 63 43 533 106 null null 67 46 null null null null null null null null 100 94 null null null null 5.028 .199 null null .198 null 52 336 .183 .9 null null null 40 49 309 318 0 163 47 116 .218 null null 4.595 null -2.2 null
13 340 331 65 44 275 287 null null 68 49 null null null null null null null null 100 100 null null null null .958 1.044 null null 1.085 null 80 341 .953 .92 null null null 40 50 323 333 0 363 48 315 1.145 null null .873 null .196 null
14 3152 829 63 43 3089 786 null null 64 45 null null null null null null null null 100 100 null null null null 3.93 .254 null null .259 null 80 362 .243 .95 null null null 40 50 338 348 0 910 47 863 .279 null null 3.579 null -1.84 null
15 205 263 62 44 143 219 null null 63 45 null null null null null null null null 100 100 null null null null .653 1.531 null null 1.679 null 80 338 1.304 .9 null null null 41 51 353 363 0 289 48 241 1.685 null null .593 null .753 null
16 345 106 60 43 285 63 null null 61 45 null null null null null null null null 100 100 null null null null 4.524 .221 null null .216 null 52 289 .195 .82 null null null 41 50 367 376 0 116 47 69 .242 null null 4.13 null -2.046 null
17 2980 563 60 41 2920 522 null null 62 43 null null null null null null null null 100 100 null null null null 5.594 .179 null null .178 null 80 404 .174 .95 null null null 41 51 383 393 0 618 45 573 .196 null null 5.096 null -2.349 null
18 275 201 63 41 212 160 null null 65 43 null null null null null null null null 100 100 null null null null 1.325 .755 null null .758 null 12 104 .61 .81 null null null 43 48 399 404 0 220 45 175 .825 null null 1.211 null -.277 null
19 1187 1371 62 43 1125 1328 null null 64 44 null null null null null null null null 97 98 null null null null .847 1.18 null null 1.155 null 80 417 1.115 .97 null null null 42 52 412 422 0 1506 47 1459 1.297 null null .771 null .375 null
20 385 295 63 44 322 251 null null 65 47 null null null null null null null null 100 100 null null null null 1.283 .78 null null .781 null 52 321 .719 .91 null null null 41 50 428 437 0 324 48 276 .857 null null 1.167 null -.222 null

Total number of rows: 24192

Table truncated, full table size 5609 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap